4KI3 | pdb_00004ki3

1.70 Angstrom resolution crystal structure of outer-membrane lipoprotein carrier protein (lolA) from Yersinia pestis CO92

PDB DOI: https://doi.org/10.2210/pdb4KI3/pdb

Classification: CHAPERONE
Organism(s): Yersinia pestis biovar Medievalis str. Harbin 35
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-01 Released: 2013-05-15
Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Kudritska, M., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

1.70 Angstrom resolution crystal structure of outer-membrane lipoprotein carrier protein (lolA) from Yersinia pestis CO92

Halavaty, A.S., Wawrzak, Z., Kudritska, M., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 245.52 kDa
Atom Count: 19,260
Modeled Residue Count: 2,103
Deposited Residue Count: 2,208
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer-membrane lipoprotein carrier protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	184	Yersinia pestis biovar Medievalis str. Harbin 35	Mutation(s): 0 Gene Names: lolA, YPC_2798

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth J] SDF format, chain R [auth D] SDF format, chain N [auth A] MOL2 format, chain X [auth J] MOL2 format, chain R [auth D] MOL2 format, chain N [auth A] mmCIF format, chain X [auth J] mmCIF format, chain R [auth D] mmCIF format, chain N [auth A]	N [auth A], R [auth D], X [auth J]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain R [auth D] Focus chain X [auth J] Interactions & Density Focus chain N [auth A] Focus chain R [auth D] Focus chain X [auth J]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth H] SDF format, chain O [auth A] MOL2 format, chain V [auth H] MOL2 format, chain O [auth A] mmCIF format, chain V [auth H] mmCIF format, chain O [auth A]	O [auth A], V [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain V [auth H] Interactions & Density Focus chain O [auth A] Focus chain V [auth H]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain W [auth I] SDF format, chain U [auth H] SDF format, chain T [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth D] SDF format, chain P [auth B] SDF format, chain M [auth A] MOL2 format, chain W [auth I] MOL2 format, chain U [auth H] MOL2 format, chain T [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] mmCIF format, chain W [auth I] mmCIF format, chain U [auth H] mmCIF format, chain T [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A]	M [auth A] P [auth B] Q [auth D] S [auth F] T [auth G] M [auth A], P [auth B], Q [auth D], S [auth F], T [auth G], U [auth H], W [auth I]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth D] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain W [auth I] Interactions & Density Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth D] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain W [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)
R-Value Observed: 0.205 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.201	α = 94.3
b = 67.13	β = 94.01
c = 132.563	γ = 120.01

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-15

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-05-15
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description