5T1P | pdb_00005t1p

Crystal structure of the putative periplasmic solute-binding protein from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb5T1P/pdb

Classification: HYDROLASE
Organism(s): Campylobacter jejuni BJ-CJGB96299
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-19 Released: 2016-09-07
Deposition Author(s): Filippova, E.V., Wawrzsak, Z., Sandoval, J., Skarina, T., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.228 (DCC)
R-Value Work:
0.176 (Depositor), 0.184 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the putative periplasmic solute-binding protein from Campylobacter jejuni

Filippova, E.V., Wawrzsak, Z., Sandoval, J., Skarina, T., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 311.61 kDa
Atom Count: 22,353
Modeled Residue Count: 2,612
Deposited Residue Count: 2,784
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, periplasmic substrate-binding protein	A, B, C, D, E A, B, C, D, E, F, G, H	348	Campylobacter jejuni BJ-CJGB96299	Mutation(s): 0 Gene Names: K680_1691

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GPE Query on GPE Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A]	J [auth A], K [auth B], L [auth C], M [auth D]	L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE C₅ H₁₄ N O₆ P JZNWSCPGTDBMEW-RXMQYKEDSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain R [auth G] SDF format, chain N [auth E] MOL2 format, chain R [auth G] MOL2 format, chain N [auth E] mmCIF format, chain R [auth G] mmCIF format, chain N [auth E]	N [auth E], R [auth G]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain N [auth E] Focus chain R [auth G] Interactions & Density Focus chain N [auth E] Focus chain R [auth G]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain P [auth F] MOL2 format, chain S [auth H] MOL2 format, chain P [auth F] mmCIF format, chain S [auth H] mmCIF format, chain P [auth F]	P [auth F], S [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain P [auth F] Focus chain S [auth H] Interactions & Density Focus chain P [auth F] Focus chain S [auth H]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain T [auth H] SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain I [auth A] MOL2 format, chain T [auth H] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain I [auth A] mmCIF format, chain T [auth H] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain I [auth A]	I [auth A], O [auth E], Q [auth F], T [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth E] Focus chain Q [auth F] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain O [auth E] Focus chain Q [auth F] Focus chain T [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.228 (DCC)
R-Value Work: 0.176 (Depositor), 0.184 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.19	α = 68.88
b = 89.276	β = 82.52
c = 100.394	γ = 70.66

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHENIX	phasing
PHENIX	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Structure summary

5T1P | pdb_00005t1p

Crystal structure of the putative periplasmic solute-binding protein from Campylobacter jejuni

Literature

Crystal structure of the putative periplasmic solute-binding protein from Campylobacter jejuni

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Biological Assembly 8

Macromolecules

Entity ID: 1

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)