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- PDB-4nf2: Crystal structure of anabolic ornithine carbamoyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 4nf2
TitleCrystal structure of anabolic ornithine carbamoyltransferase from Bacillus anthracis in complex with carbamoyl phosphate and L-norvaline
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / carbamoyl phosphate / L-ornithine
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / L-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 / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain ...Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / NORVALINE / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsShabalin, I.G. / Handing, K. / Cymborowski, M.T. / 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 and kinetic properties of anabolic ornithine carbamoyltransferase from human pathogens Vibrio vulnificus and Bacillus anthracis
Authors: Shabalin, I.G. / Handing, K. / Cymborowski, M.T. / Stam, J. / Winsor, J. / Shuvalova, L. / Anderson, W.F. / Minor, W.
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,52614
Polymers114,5743
Non-polymers95211
Water15,241846
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-28 kcal/mol
Surface area32850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.893, 99.893, 118.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 5 - 311 / Label seq-ID: 29 - 335

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ornithine carbamoyltransferase / OTCase


Mass: 38191.426 Da / Num. of mol.: 3 / Mutation: G86X, 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
#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Chemical ChemComp-NVA / NORVALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 20 mM L-norvaline, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: Index #79 (0.1 M Bis-Tris pH 6.5, ...Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 20 mM L-norvaline, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: Index #79 (0.1 M Bis-Tris pH 6.5, 0.2 M NH4 Acetate,25% w/v PEG 3350). Mixed as 0.2 ul + 0.2 ul., VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2012 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGT / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 105890 / Num. obs: 105149 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Χ2: 1.173 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.74-1.773.40.602252290.6020.8799.8
1.77-1.83.40.49251980.90199.7
1.8-1.843.50.39552360.89299.6
1.84-1.873.50.32351840.88699.5
1.87-1.923.50.28352390.91999.4
1.92-1.963.50.22551810.9999.4
1.96-2.013.50.19952041.02199.2
2.01-2.063.50.15651961.10399
2.06-2.123.50.13451971.16399.2
2.12-2.193.50.1152221.19799
2.19-2.273.50.09352071.22499
2.27-2.363.50.07752101.17899.1
2.36-2.473.50.06552531.20699.4
2.47-2.63.50.06152391.40299.4
2.6-2.763.50.05352811.43299.3
2.76-2.983.50.04752821.75999.6
2.98-3.273.50.03653161.66999.8
3.27-3.753.50.02753651.342100
3.75-4.723.50.02153950.99199.8
4.72-503.40.02755151.26297.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
CCP4phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H31

4h31


Resolution: 1.74→29.23 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1727 / WRfactor Rwork: 0.1461 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9034 / SU B: 3.48 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0906 / SU Rfree: 0.0867 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1701 5231 5 %RANDOM
Rwork0.1454 ---
all0.1466 105456 --
obs0.1466 104782 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 116.21 Å2 / Biso mean: 32.3437 Å2 / Biso min: 14.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20 Å2
2---1.41 Å2-0 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.74→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7212 0 53 846 8111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197521
X-RAY DIFFRACTIONr_bond_other_d0.0080.027266
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.96410193
X-RAY DIFFRACTIONr_angle_other_deg1.278316776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06925.578346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.616151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9041521
X-RAY DIFFRACTIONr_chiral_restr0.1030.21159
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028519
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021666
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A198190.07
12B198190.07
21A196300.09
22C196300.09
31B195580.09
32C195580.09
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 387 -
Rwork0.229 7294 -
all-7681 -
obs-7294 99.7 %
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)
10.80020.1530.0781.4318-0.01660.564-0.0282-0.08220.13640.023-0.06020.2437-0.0105-0.11970.08840.03380.0064-0.01990.0833-0.0220.084813.75311.0910.877
22.5302-0.97490.71171.2466-0.8921.5272-0.13110.29740.66770.034-0.102-0.1445-0.2569-0.09110.23310.11330.0124-0.10610.07860.08150.25916.62131.3120.328
36.28176.04060.100417.98881.41075.8908-0.48930.7872-0.2519-1.5604-0.0061-1.49830.69860.70670.49540.42630.05760.1380.43190.27690.384331.42826.35-11.718
42.85170.12830.3681.7681-0.4971.5859-0.19410.03360.71080.0647-0.1378-0.1059-0.30060.08650.33190.0941-0.0176-0.13340.01440.03030.278626.07129.5128.926
51.2119-0.10460.0551.5552-0.04521.2532-0.072-0.20450.13580.32980.02060.0129-0.0746-0.09240.05140.14860.0192-0.01580.0967-0.03710.020939.9735.14730.587
61.3679-0.2250.24681.06430.01220.2585-0.0667-0.03170.19030.1288-0.001-0.1445-0.0210.01610.06770.09960.0081-0.03310.0807-0.01520.049845.7025.96221.758
71.18140.0914-0.08021.32940.10910.8958-0.0228-0.0265-0.03470.11630.0107-0.31950.05470.14150.01210.09630.0285-0.03830.08440.00040.080457.09-7.29122.275
816.45957.93280.060114.6225-7.51486.38560.2896-0.61781.19071.0144-0.03450.6567-0.7716-0.1084-0.25510.24420.05180.04380.1159-0.10.148536.80711.36933.525
91.37890.27480.61020.54050.30260.68680.0487-0.2083-0.09150.163-0.03910.07590.1117-0.1381-0.00960.1305-0.04190.01120.09960.01870.027421.547-14.51118.438
101.32680.00760.11931.5310.58311.74620.0601-0.1047-0.21270.16-0.03950.15280.2865-0.1289-0.02060.1056-0.0724-0.01570.06270.01830.09410.19-29.2124.032
115.88123.42527.15096.08867.994513.8112-0.17660.7872-0.3341-0.4860.7822-0.5334-0.47661.2919-0.60560.1062-0.0820.0430.1592-0.05460.067220.809-18.623-8.95
120.79060.15330.38781.45080.67161.55520.0033-0.1314-0.00150.0268-0.10850.2825-0.004-0.25270.10520.0374-0.0378-0.00410.0981-0.01070.06716.309-15.6374.379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 134
2X-RAY DIFFRACTION2A135 - 237
3X-RAY DIFFRACTION3A238 - 250
4X-RAY DIFFRACTION4A251 - 311
5X-RAY DIFFRACTION5B5 - 66
6X-RAY DIFFRACTION6B67 - 190
7X-RAY DIFFRACTION7B191 - 304
8X-RAY DIFFRACTION8B305 - 311
9X-RAY DIFFRACTION9C5 - 148
10X-RAY DIFFRACTION10C149 - 232
11X-RAY DIFFRACTION11C233 - 248
12X-RAY DIFFRACTION12C249 - 311

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