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- PDB-1js1: Crystal Structure of a new transcarbamylase from the anaerobic ba... -

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Basic information

Entry
Database: PDB / ID: 1js1
TitleCrystal Structure of a new transcarbamylase from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution
ComponentsTranscarbamylase
KeywordsTRANSFERASE / alpha/beta topology / two domains
Function / homology
Function and homology information


N-succinylornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / amino acid binding
Similarity search - Function
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
PHOSPHATE ION / N-succinylornithine carbamoyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsShi, D. / Gallegos, R. / DePonte III, J. / Morizono, H. / Yu, X. / Allewell, N.M. / Malamy, M. / Tuchman, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution.
Authors: Shi, D. / Gallegos, R. / DePonte III, J. / Morizono, H. / Yu, X. / Allewell, N.M. / Malamy, M. / Tuchman, M.
History
DepositionAug 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2013Group: Data collection
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Transcarbamylase
Y: Transcarbamylase
Z: Transcarbamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1116
Polymers111,8273
Non-polymers2853
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-66 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.411, 153.411, 94.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transcarbamylase


Mass: 37275.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8A1E9, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases
#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.: 422 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.9 Mammonium sulfate1reservoir
2125 mM1dropNaCl
320 mMTris-Cl1drop
41 mMEDTA1drop
516 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Jan 1, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 1608840 / Num. obs: 74187 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4454 / % possible all: 88.1
Reflection
*PLUS
% possible obs: 96.8 % / Num. measured all: 1608840 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.13 Å / % possible obs: 88.1 % / Rmerge(I) obs: 0.421

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→27.28 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4810860.57 / Data cutoff high rms absF: 4810860.57 / 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
Rfree0.252 7481 10.1 %RANDOM
Rwork0.206 ---
all0.211 74187 --
obs0.206 74134 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.573 Å2 / ksol: 0.364869 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 15 422 8177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 1177 10.4 %
Rwork0.251 10105 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Rfactor all: 0.211 / Rfactor obs: 0.206 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / Rfactor Rwork: 0.251 / Num. reflection Rwork: 10106

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