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- PDB-2g7m: Crystal structure of B. fragilis N-succinylornithine transcarbamy... -

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Basic information

Entry
Database: PDB / ID: 2g7m
TitleCrystal structure of B. fragilis N-succinylornithine transcarbamylase P90E mutant complexed with carbamoyl phosphate and N-acetylnorvaline
Componentsputative ornithine carbamoyltransferase
KeywordsTRANSFERASE / Alpha/beta
Function / homology
Function and homology information


N-succinylornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / 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-ACETYL-L-NORVALINE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / : / N-succinylornithine carbamoyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShi, D. / Yu, X. / Roth, L. / Morizono, H. / Allewell, N.M. / Tuchman, M.
CitationJournal: Protein Sci. / Year: 2007
Title: A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase.
Authors: Shi, D. / Yu, X. / Cabrera-Luque, J. / Chen, T.Y. / Roth, L. / Morizono, H. / Allewell, N.M. / Tuchman, M.
History
DepositionFeb 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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)233,96620
Polymers231,9726
Non-polymers1,99314
Water3,099172
1
X: putative ornithine carbamoyltransferase
Y: putative ornithine carbamoyltransferase
Z: putative ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,98310
Polymers115,9863
Non-polymers9977
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-75 kcal/mol
Surface area32960 Å2
MethodPISA
2
C: putative ornithine carbamoyltransferase
D: putative ornithine carbamoyltransferase
E: putative ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,98310
Polymers115,9863
Non-polymers9977
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-75 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.654, 156.654, 120.201
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: 38662.047 Da / Num. of mol.: 6 / Mutation: P90E, T242L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: argF' / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 60491451, UniProt: Q64Z33*PLUS, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases
#2: Chemical
ChemComp-AN0 / N-ACETYL-L-NORVALINE


Mass: 159.183 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H13NO3
#3: Chemical
ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5.5
Details: 1.5M ammonium sulfate, 100mM Bis-tris, pH 5.5, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 2006 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 64435 / Num. obs: 64177 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 9.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6363 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FG7

2fg7


Resolution: 2.9→19.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 825751.5 / 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
Rfree0.236 3234 5.1 %RANDOM
Rwork0.218 ---
all0.219 64177 --
obs0.218 64024 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.658 Å2 / ksol: 0.325694 e/Å3
Displacement parametersBiso mean: 57.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15488 0 124 172 15784
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 507 4.8 %
Rwork0.348 10073 -
obs--98.8 %
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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