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- PDB-2yvq: Crystal structure of MGS domain of carbamoyl-phosphate synthetase... -

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Basic information

Entry
Database: PDB / ID: 2yvq
TitleCrystal structure of MGS domain of carbamoyl-phosphate synthetase from homo sapiens
ComponentsCarbamoyl-phosphate synthase
KeywordsLIGASE / conserved hypothetical protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / carbamoyl-phosphate synthase (ammonia) activity / nitric oxide metabolic process / modified amino acid binding / triglyceride catabolic process / homocysteine metabolic process / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / carbamoyl-phosphate synthase (ammonia) activity / nitric oxide metabolic process / modified amino acid binding / triglyceride catabolic process / homocysteine metabolic process / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / cellular response to ammonium ion / Urea cycle / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / response to food / cellular response to fibroblast growth factor stimulus / response to growth hormone / glutamate binding / midgut development / response to zinc ion / response to dexamethasone / response to starvation / mitochondrial nucleoid / glutamine metabolic process / cellular response to glucagon stimulus / response to amine / small molecule binding / potassium ion binding / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / cellular response to cAMP / phospholipid binding / response to toxic substance / vasodilation / endopeptidase activity / mitochondrial inner membrane / response to lipopolysaccharide / mitochondrial matrix / response to xenobiotic stimulus / calcium ion binding / protein-containing complex binding / nucleolus / protein-containing complex / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain ...Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Glutamine amidotransferase class-I / Glutamine amidotransferase / Carbamoyl-phosphate synthase subdomain signature 1. / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbamoyl-phosphate synthase [ammonia], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsXie, Y. / Ihsanawati / Kishishita, S. / Murayama, K. / Takemoto, C. / Shirozu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of MGS domain of carbamoyl-phosphate synthetase from homo sapiens
Authors: Xie, Y. / Ihsanawati / Kishishita, S. / Murayama, K. / Takemoto, C. / Shirozu, M. / Yokoyama, S.
History
DepositionApr 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbamoyl-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)15,6091
Polymers15,6091
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbamoyl-phosphate synthase

A: Carbamoyl-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)31,2172
Polymers31,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3200 Å2
ΔGint-23 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.505, 50.505, 97.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Carbamoyl-phosphate synthase / Carbamoyl-phosphate synthetase I / CPSase I


Mass: 15608.656 Da / Num. of mol.: 1 / Fragment: MGS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Plasmid: PK060110-54-MD01
References: UniProt: P31327, carbamoyl-phosphate synthase (ammonia)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M (NH4)2SO4, 0.1M MES, 10%(V/V) dioxane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2006 / Details: Mirrors
RadiationMonochromator: silikon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 10442 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 10.7466 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 37.2
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 8.25 / Num. unique all: 1398 / Rsym value: 0.213 / % possible all: 94.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→26.11 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 914355.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1023 10.5 %RANDOM
Rwork0.232 ---
obs0.232 9705 91.9 %-
all-10422 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.1097 Å2 / ksol: 0.376183 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-5.33 Å25.36 Å20 Å2
2--5.33 Å20 Å2
3----10.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.98→26.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 0 76 1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it9.462
X-RAY DIFFRACTIONc_scangle_it8.042.5
LS refinement shellResolution: 1.98→2.1 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 134 10.6 %
Rwork0.265 1136 -
obs--74 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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