3DTD

Crystal structure of invasion associated protein b from bartonella henselae

PDB DOI: https://doi.org/10.2210/pdb3DTD/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bartonella henselae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-14 Released: 2008-09-09
Deposition Author(s): Patskovsky, Y., Ozyurt, S., Freeman, J., Slocombe, A., Groshong, C., Koss, J., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.265 (Depositor), 0.260 (DCC)
R-Value Work:
0.235 (Depositor), 0.230 (DCC)
R-Value Observed:
0.236 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Invasion Associated Protein B from Bartonella Henselae.

Patskovsky, Y., Ozyurt, S., Freeman, J., Slocombe, A., Groshong, C., Koss, J., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 227.76 kDa
Atom Count: 13,760
Modelled Residue Count: 1,734
Deposited Residue Count: 2,100
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Invasion-associated protein B	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	175	Bartonella henselae	Mutation(s): 0 Gene Names: invB, BH01650
UniProt
Find proteins for A0A0H3LVG3 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore A0A0H3LVG3 Go to UniProtKB: A0A0H3LVG3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3LVG3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth K] SDF format, chain CA [auth L] SDF format, chain DA [auth L] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth H] SDF format, chain W [auth H] SDF format, chain X [auth I] SDF format, chain Y [auth I] SDF format, chain Z [auth I] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth K] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth L] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth I] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth K] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth L] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain V [auth H] mmCIF format, chain W [auth H] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth I]	AA [auth J] BA [auth K] CA [auth L] DA [auth L] M [auth B] AA [auth J], BA [auth K], CA [auth L], DA [auth L], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth D], T [auth F], U [auth G], V [auth H], W [auth H], X [auth I], Y [auth I], Z [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.265 (Depositor), 0.260 (DCC)
R-Value Work: 0.235 (Depositor), 0.230 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.707	α = 90
b = 139.951	β = 90
c = 179.075	γ = 90

Software Package:

Software Name	Purpose
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-10-16
Changes: Data collection, Database references, Refinement description, Structure summary