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- PDB-1vlv: Crystal structure of Ornithine carbamoyltransferase (TM1097) from... -

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Basic information

Entry
Database: PDB / ID: 1vlv
TitleCrystal structure of Ornithine carbamoyltransferase (TM1097) from Thermotoga maritima at 2.25 A resolution
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / TM1097 / ORNITHINE CARBAMOYLTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline 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
PHOSPHATE ION / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ornithine carbamoyltransferase (TM1097) from Thermotoga maritima at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1554
Polymers36,8701
Non-polymers2853
Water1,69394
1
A: Ornithine carbamoyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)445,86448
Polymers442,44512
Non-polymers3,41936
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation28_565x,-y+3/2,-z+1/21
crystal symmetry operation31_664-z+1,-x+3/2,y-1/21
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation51_655-x+3/2,y,-z+1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation60_664-y+3/2,-z+1,x-1/21
crystal symmetry operation74_665-x+3/2,-y+3/2,z1
crystal symmetry operation78_566z+1/2,-x+3/2,-y+11
crystal symmetry operation82_656-y+3/2,z+1/2,-x+11
Buried area60820 Å2
ΔGint-323 kcal/mol
Surface area105440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)210.339, 210.339, 210.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-315-

PO4

21A-315-

PO4

31A-316-

PO4

41A-316-

PO4

51A-394-

HOH

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Components

#1: Protein Ornithine carbamoyltransferase / OTCase


Mass: 36870.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: argF / Production host: Escherichia coli (E. coli) / References: UniProt: P96108, ornithine carbamoyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.75 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.1
Details: 0.2% MPD, 0.2M NH4OAc, 0.1M Na,K-Phosphate pH 6.1, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Sep 20, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→63.32 Å / Num. obs: 19349 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 58.84 Å2 / Rsym value: 0.071 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5014 / Num. unique all: 1366 / Rsym value: 0.734 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a1s

1a1s


Resolution: 2.25→63.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.955 / SU B: 12.355 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1), HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2), THE DENSITY BETWEEN 235-244 IS WEAK AND IT IS NOT POSSIBLE TO BUILD THE MISSING RESIDUES INTO IT. 3), TWO PO4 ANIONS ARE LOCATED AT ...Details: 1), HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2), THE DENSITY BETWEEN 235-244 IS WEAK AND IT IS NOT POSSIBLE TO BUILD THE MISSING RESIDUES INTO IT. 3), TWO PO4 ANIONS ARE LOCATED AT THE THREE-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS AT THE INTERFACE BETWEEN THREE MONOMERS. THE P AND O ATOMS ON THESE RESIDUES WERE MODELED WITH OCCUPANCIES OF 0.33.
RfactorNum. reflection% reflectionSelection details
Rfree0.21528 986 5.1 %RANDOM
Rwork0.18917 ---
obs0.19049 18186 98.83 %-
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 mean: 47.765 Å2
Refinement stepCycle: LAST / Resolution: 2.25→63.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 15 94 2513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222458
X-RAY DIFFRACTIONr_bond_other_d0.0010.022249
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9633317
X-RAY DIFFRACTIONr_angle_other_deg0.88235210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1185306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40723.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65515439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3211518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.2140.2473
X-RAY DIFFRACTIONr_nbd_other0.1820.22202
X-RAY DIFFRACTIONr_nbtor_other0.0870.21428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.214
X-RAY DIFFRACTIONr_mcbond_it0.7311.51571
X-RAY DIFFRACTIONr_mcbond_other0.1541.5628
X-RAY DIFFRACTIONr_mcangle_it1.14922457
X-RAY DIFFRACTIONr_scbond_it1.8233988
X-RAY DIFFRACTIONr_scangle_it2.7354.5860
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21154
LS refinement shellResolution: 2.25→2.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 65 4.85 %
Rwork0.293 1276 -
obs--96.41 %
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)
12.47650.5205-0.47992.07630.37591.9867-0.0324-0.1881-0.23720.21590.0013-0.30390.11820.24280.0311-0.24650.0125-0.0413-0.07870.0037-0.1561186.4236152.698865.1229
27.9252-7.0483-3.974612.03118.22715.81410.1606-0.27630.2241-0.2748-0.0036-0.1908-0.57690.2854-0.157-0.1828-0.063-0.0532-0.0323-0.0123-0.1812186.9914164.675775.5007
34.90310.2720.29192.4983-0.58714.26590.1088-0.38260.19370.2639-0.2066-0.4037-0.38161.08140.0979-0.1676-0.1617-0.14710.2923-0.05540.0251199.5501166.347680.6084
48.17731.2670.28252.6751-0.07813.70470.1213-1.22860.00060.5323-0.1954-0.3469-0.05530.75550.0742-0.0196-0.061-0.15310.3476-0.0501-0.1729190.847162.521192.651
53.9967-0.4772-0.20321.51150.0788.2463-0.0268-0.2097-0.03710.1528-0.0438-0.14030.1436-0.17340.0706-0.2731-0.0444-0.0424-0.1946-0.0149-0.1802180.8309159.485871.0387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11-4 - 1348 - 146
22135 - 149147 - 161
33150 - 234162 - 246
44245 - 292257 - 304
55293 - 313305 - 325

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