4NAS | pdb_00004nas

The crystal structure of a rubisco-like protein (MtnW) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

PDB DOI: https://doi.org/10.2210/pdb4NAS/pdb

Classification: LYASE
Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-10-22 Released: 2013-11-13
Deposition Author(s): Tan, K., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.251 (Depositor), 0.249 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a rubisco-like protein (MtnW) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446.

Tan, K., Li, H., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 178.08 kDa
Atom Count: 12,421
Modeled Residue Count: 1,584
Deposited Residue Count: 1,636
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose-bisphosphate carboxylase	A, B, C, D	409	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0 Gene Names: Aaci_0096 EC: 4.1.1.39
UniProt
Find proteins for C8WQ56 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore C8WQ56 Go to UniProtKB: C8WQ56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C8WQ56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], J [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth B] L [auth B] N [auth C] G [auth A], H [auth A], K [auth B], L [auth B], N [auth C], O [auth C], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.251 (Depositor), 0.249 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.763	α = 90
b = 175.671	β = 107.67
c = 83.653	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-11-13
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

4NAS | pdb_00004nas

The crystal structure of a rubisco-like protein (MtnW) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

Literature

The crystal structure of a rubisco-like protein (MtnW) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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