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- PDB-2fg6: N-succinyl-L-ornithine transcarbamylase from B. fragilis complexe... -

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Basic information

Entry
Database: PDB / ID: 2fg6
TitleN-succinyl-L-ornithine transcarbamylase from B. fragilis complexed with sulfate and N-succinyl-L-norvaline
Componentsputative ornithine carbamoyltransferase
KeywordsTRANSFERASE / alpha/beta
Function / homology
Function and homology information


N-succinylornithine carbamoyltransferase / ornithine carbamoyltransferase activity / L-arginine biosynthetic process / amino acid binding
Similarity search - Function
N-succinylornithine carbamoyltransferase ArgF'-like / Aspartate/ornithine carbamoyltransferase / 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
N-(3-CARBOXYPROPANOYL)-L-NORVALINE / N-succinylornithine carbamoyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShi, D. / Yu, X. / Malamy, M.H. / Allewell, N.M. / Mendel, T.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis.
Authors: Shi, D. / Morizono, H. / Cabrera-Luque, J. / Yu, X. / Roth, L. / Malamy, M.H. / Allewell, N.M. / Tuchman, M.
History
DepositionDec 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: 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 1.5Aug 30, 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

Downloads & links

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Assembly

Deposited unit
X: putative ornithine carbamoyltransferase
Y: putative ornithine carbamoyltransferase
Z: putative ornithine carbamoyltransferase
C: putative ornithine carbamoyltransferase
D: putative ornithine carbamoyltransferase
E: putative ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,85220
Polymers231,7806
Non-polymers2,07214
Water5,693316
1
X: putative ornithine carbamoyltransferase
Y: putative ornithine carbamoyltransferase
Z: putative ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,92610
Polymers115,8903
Non-polymers1,0367
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-115 kcal/mol
Surface area33030 Å2
MethodPISA
2
C: putative ornithine carbamoyltransferase
D: putative ornithine carbamoyltransferase
E: putative ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,92610
Polymers115,8903
Non-polymers1,0367
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-123 kcal/mol
Surface area33320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24730 Å2
ΔGint-243 kcal/mol
Surface area62490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.703, 155.703, 120.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological unit is a trimer generated by chain X, Y and Z, or C, D and E

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Components

#1: Protein
putative ornithine carbamoyltransferase


Mass: 38630.051 Da / Num. of mol.: 6 / Mutation: T242L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: argF' / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5LI27, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-SN0 / N-(3-CARBOXYPROPANOYL)-L-NORVALINE


Mass: 217.219 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H15NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.5 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 18, 2005
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 70821 / Num. obs: 70538 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 69.7 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7055 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CCP4(TRUNCATE)data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JS1

1js1


Resolution: 2.8→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 898791.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3585 5.1 %RANDOM
Rwork0.216 ---
all0.218 70538 --
obs0.216 70401 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.3641 Å2 / ksol: 0.32321 e/Å3
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.45 Å20 Å20 Å2
2---5.45 Å20 Å2
3---10.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15532 0 130 316 15978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 598 5.1 %
Rwork0.332 11034 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top

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