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- PDB-4ep1: Crystal structure of anabolic ornithine carbamoyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 4ep1
TitleCrystal structure of anabolic ornithine carbamoyltransferase from Bacillus anthracis
ComponentsOrnithine carbamoyltransferaseOrnithine transcarbamylase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / trimer / ornithine carbamoyltransferase
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function
Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase ...Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsShabalin, I.G. / Mikolajczak, K. / Stam, J. / Winsor, J. / Shuvalova, L. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structures of anabolic ornithine carbamoyltransferase from Bacillus anthracis
Authors: Shabalin, I.G. / Mikolajczak, K. / Stam, J. / Winsor, J. / Shuvalova, L. / Anderson, W.F. / Minor, W.
History
DepositionApr 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)76,2412
Polymers76,2412
Non-polymers00
Water0
1
A: Ornithine carbamoyltransferase

A: Ornithine carbamoyltransferase

A: Ornithine carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)114,3613
Polymers114,3613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4250 Å2
ΔGint-32 kcal/mol
Surface area34320 Å2
MethodPISA
2
B: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)114,3613
Polymers114,3613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area4770 Å2
ΔGint-25 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.438, 182.438, 182.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 312
2010B4 - 312

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Components

#1: Protein Ornithine carbamoyltransferase / Ornithine transcarbamylase / OTCase


Mass: 38120.352 Da / Num. of mol.: 2 / Mutation: K191R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: argF, BAS4036, BA_4351, GBAA_4351 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81M99, ornithine carbamoyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl and 5 mM b-mercaptoethanol. Precipitant: 0.2M potassium sodium tartrate, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 16913 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 87.7 Å2 / Rmerge(I) obs: 0.163 / Rsym value: 0.163 / Net I/σ(I): 22.8
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 3.1 / Num. unique all: 793 / Rsym value: 0.931 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SwissModel-generated model

Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 1 / SU B: 36.408 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 856 5.1 %RANDOM
Rwork0.1704 ---
all0.1724 16102 --
obs0.1724 16002 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 186.26 Å2 / Biso mean: 84.0478 Å2 / Biso min: 48.07 Å2
Refinement stepCycle: LAST / Resolution: 3.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4591 0 0 0 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024677
X-RAY DIFFRACTIONr_bond_other_d0.0040.023020
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9586344
X-RAY DIFFRACTIONr_angle_other_deg1.12737453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4625.459207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53515799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.3491512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025182
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02866
Refine LS restraints NCS

Ens-ID: 1 / Number: 10485 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.07 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 54 -
Rwork0.249 955 -
all-1009 -
obs-955 92.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2239-0.3615-0.36313.6439-1.14311.77220.15760.09410.14510.19-0.17930.1368-0.03610.09710.02170.1740.12930.00090.1317-0.0130.03544.843-21.81112.405
22.83441.10550.9974.46751.34081.71370.23630.1803-0.20840.2101-0.1743-0.23260.0161-0.0752-0.0620.20030.1456-0.060.1332-0.03390.02991.204-66.34210.249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 312
2X-RAY DIFFRACTION2B4 - 312

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