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

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Basic information

Entry
Database: PDB / ID: 4jfr
TitleCrystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate
ComponentsOrnithine carbamoyltransferaseOrnithine transcarbamylase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / anabolic ornithine carbamoyltransferase / carbamoyl phospate / ornithine
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 / 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 / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsShabalin, I.G. / Winsor, J. / Grimshaw, S. / Osinski, T. / Bajor, J. / Chordia, M.D. / 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. / Winsor, J. / Grimshaw, S. / Minor, W.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr2_auth_seq_id / _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)119,3399
Polymers118,9263
Non-polymers4136
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-75 kcal/mol
Surface area35970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.343, 80.916, 177.637
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: 0 / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA-1 - 33323 - 357
21ASNASNBB-1 - 33323 - 357
12METMETAA1 - 33325 - 357
22METMETCC1 - 33325 - 357
13METMETBB1 - 33325 - 357
23METMETCC1 - 33325 - 357

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ornithine carbamoyltransferase / Ornithine transcarbamylase / OTCase


Mass: 39641.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: argF, VV1_1466 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DCF5, ornithine carbamoyltransferase
#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Carbamoyl phosphate


Mass: 141.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350, 0.2M ...Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350, 0.2M Magnesium Chloride, VAPOR DIFFUSION, HANGING 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, 2011 / Details: Be-lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGT / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. all: 62876 / Num. obs: 62625 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Χ2: 1.705 / Net I/σ(I): 35.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.17-2.214.60.7822307020.98199.1
2.21-2.255.30.75831190.981100
2.25-2.296.30.7230431.005100
2.29-2.346.50.63631021.015100
2.34-2.396.60.52631181.029100
2.39-2.446.60.4531021.091100
2.44-2.516.60.37231001.084100
2.51-2.576.60.31131041.132100
2.57-2.656.60.25231071.182100
2.65-2.736.60.20531511.242100
2.73-2.836.60.17531021.399100
2.83-2.956.60.13531211.566100
2.95-3.086.60.11131351.90399.8
3.08-3.246.60.08931532.05699.8
3.24-3.446.50.07131002.38799.5
3.44-3.716.40.06131782.72899.3
3.71-4.086.10.05431233.1598.7
4.08-4.675.90.04731113.13998.1
4.67-5.896.10.0432222.64399
5.89-505.80.03533642.31498.9

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Processing

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

4h31


Resolution: 2.17→38.96 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.1659 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.854 / SU B: 11.109 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2066 / SU Rfree: 0.1676 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 3172 5.1 %RANDOM
Rwork0.1708 ---
all0.1726 62834 --
obs0.1726 62539 99.53 %-
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: 137.51 Å2 / Biso mean: 58.1717 Å2 / Biso min: 29 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3---1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.17→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7787 0 20 272 8079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197957
X-RAY DIFFRACTIONr_bond_other_d0.0070.027562
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.95210751
X-RAY DIFFRACTIONr_angle_other_deg1.232317373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88751009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61125.259367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.932151377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5011533
X-RAY DIFFRACTIONr_chiral_restr0.0950.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029170
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021827
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A204570.1
12B204570.1
21A196540.12
22C196540.12
31B197740.11
32C197740.11
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 240 -
Rwork0.269 4254 -
all-4494 -
obs-4254 99.07 %
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)
11.81080.330.67671.16640.29510.8716-0.09370.04080.1793-0.09120.0715-0.03-0.0770.07750.02220.0159-0.03390.00990.1487-0.06430.11555.18713.266-14.08
22.57010.5571-0.05691.02490.0240.9387-0.1683-0.58970.7587-0.0579-0.08950.2454-0.1474-0.10270.25770.05760.0529-0.0620.25-0.27880.408-9.74625.458-0.962
32.63030.07560.18570.74540.55431.0134-0.1977-0.05560.5586-0.1499-0.07250.216-0.164-0.16490.27030.05930.0514-0.08340.1382-0.12240.2979-16.60821.147-12.965
41.83750.01810.07991.4080.54081.4236-0.10960.26230.21-0.27340.02740.1644-0.0965-0.02380.08210.0972-0.0196-0.06120.2430.01550.0521-12.3434.28-36.24
54.00670.04730.11512.33930.83611.2029-0.22520.2682-0.3104-0.2968-0.0020.56090.0024-0.31220.22720.0992-0.05-0.0710.4615-0.11630.1941-26.691-14.522-43.403
62.94530.19590.53433.0186-0.10631.0383-0.03990.091-0.64280.10160.13990.03450.0084-0.0695-0.10.12360.0045-0.01010.3129-0.03750.1479-14.063-17.415-36.777
71.7773-0.32560.98593.24160.34362.23010.14830.4511-0.2594-0.2690.2553-0.66630.29840.8231-0.40370.07820.0940.03030.5323-0.28430.317821.286-14.787-29.022
82.32540.9361.03583.02690.7272.78660.1130.149-0.17440.02530.1366-0.1195-0.06730.0006-0.24950.03620.00950.01550.2291-0.080.07485.067-6.885-26.129
91.34750.30330.90311.09460.21932.24270.28010.091-0.520.14070.1495-0.31090.37590.3069-0.42960.09520.0946-0.13440.2129-0.09440.271515.351-19.502-11.798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 149
2X-RAY DIFFRACTION2A150 - 252
3X-RAY DIFFRACTION3A253 - 334
4X-RAY DIFFRACTION4B-5 - 139
5X-RAY DIFFRACTION5B140 - 270
6X-RAY DIFFRACTION6B271 - 334
7X-RAY DIFFRACTION7C1 - 39
8X-RAY DIFFRACTION8C40 - 88
9X-RAY DIFFRACTION9C89 - 334

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