4GB5 | pdb_00004gb5

Crystal structure of Kfla4162 protein from Kribbella flavida

PDB DOI: https://doi.org/10.2210/pdb4GB5/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Kribbella flavida DSM 17836
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-26 Released: 2012-09-26
Deposition Author(s): Michalska, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.180 (Depositor), 0.190 (DCC)
R-Value Work:
0.144 (Depositor), 0.157 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Kfla4162 protein from Kribbella flavida (CASP Target)

Michalska, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 17.94 kDa
Atom Count: 1,353
Modeled Residue Count: 148
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	159	Kribbella flavida DSM 17836	Mutation(s): 0 Gene Names: Kfla_4162
UniProt
Find proteins for D2PTS5 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PTS5 Go to UniProtKB: D2PTS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2PTS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.180 (Depositor), 0.190 (DCC)
R-Value Work: 0.144 (Depositor), 0.157 (DCC)
R-Value Observed: 0.146 (Depositor)

Diffraction Data:

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.948	α = 90
b = 57.948	β = 90
c = 81.605	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

4GB5 | pdb_00004gb5

Crystal structure of Kfla4162 protein from Kribbella flavida

Literature

Crystal structure of Kfla4162 protein from Kribbella flavida (CASP Target)

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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