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- PDB-1a9x: CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HY... -

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Entry
Database: PDB / ID: 1a9x
TitleCARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS
Components(CARBAMOYL PHOSPHATE SYNTHETASE ...) x 2
KeywordsAMIDOTRANSFERASE / THIOESTER
Function / homologyCarbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Class I glutamine amidotransferase-like / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain ...Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Class I glutamine amidotransferase-like / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Pre-ATP-grasp domain superfamily / Glutamine amidotransferase / Methylglyoxal synthase-like domain superfamily / Glutamine amidotransferase class-I / Carbamoyl-phosphate synthase small chain, CPSase domain / MGS-like domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthase subdomain signature 2. / ATP-grasp fold profile. / Glutamine amidotransferase type 1 domain profile. / MGS-like domain profile. / carbamoyl-phosphate synthase complex / pyrimidine nucleobase biosynthetic process / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl phosphate biosynthetic process / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / urea cycle / arginine biosynthetic process / glutamine metabolic process / cellular amino acid biosynthetic process / 'de novo' UMP biosynthetic process / amino acid binding / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to amino acid stimulus / nucleotide binding / ATP binding / metal ion binding / cytosol / cytoplasm / Carbamoyl-phosphate synthase small chain / Carbamoyl-phosphate synthase large chain / Carbamoyl-phosphate synthase small chain
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.8 Å resolution
AuthorsThoden, J. / Holden, H.
CitationJournal: Biochemistry / Year: 1998
Title: Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.
Authors: Thoden, J.B. / Miran, S.G. / Phillips, J.C. / Howard, A.J. / Raushel, F.M. / Holden, H.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 14, 1998 / Release: Oct 21, 1998
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 21, 1998Structure modelrepositoryInitial release
1.1Mar 10, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
1.3Mar 14, 2018Structure modelDatabase referencesstruct_ref_seq_dif_struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
B: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
C: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
D: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
E: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
F: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
G: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
H: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,640111
Polyers636,8458
Non-polymers8,795103
Water81,5724528
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
B: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polyers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8760
ΔGint (kcal/M)-77
Surface area (Å2)46650
MethodPISA,PQS
3
G: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
H: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polyers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8710
ΔGint (kcal/M)-76
Surface area (Å2)46880
MethodPISA,PQS
4
C: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
D: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polyers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8740
ΔGint (kcal/M)-74
Surface area (Å2)46920
MethodPISA,PQS
5
E: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
F: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,33927
Polyers159,2112
Non-polymers2,12725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8640
ΔGint (kcal/M)-72
Surface area (Å2)46700
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)152.100, 164.400, 332.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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CARBAMOYL PHOSPHATE SYNTHETASE ... , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)


Mass: 117956.656 Da / Num. of mol.: 4 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P00968
#2: Protein/peptide
CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)


Mass: 41254.520 Da / Num. of mol.: 4 / Mutation: H353N / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P00907, UniProt: P0A6F1*PLUS

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Non-polymers , 8 types, 4631 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Formula: PO4 / Phosphate
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Formula: Mn / Manganese
#5: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 32 / Formula: K / Potassium
#6: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 28 / Formula: Cl / Chloride
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#8: Chemical
ChemComp-ORN / L-ornithine


Mass: 132.161 Da / Num. of mol.: 4 / Formula: C5H12N2O2 / Ornithine
#9: Chemical
ChemComp-NET / TETRAETHYLAMMONIUM ION


Mass: 130.251 Da / Num. of mol.: 4 / Formula: C8H20N / Tetraethylammonium
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4528 / Formula: H2O / Water

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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: 3.25 / Density percent sol: 62 %
Crystal growpH: 7.4
Details: 0.65M NET4CL 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 THEN SOAKED INTO: 1.4M NET4CL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL
Crystal grow
*PLUS
Temp: 277 K / pH: 8 / Method: batch method / Details: Thoden, J.B., (1995) Acta Crysta., D51, 827.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
1100 mM11KCl
20.5 mML-ornithine11
30.5 mM11MnCl2
42.5 mMADP11
58 %PEG800011
60.65 Mtetraethylammonium chloride11
712.5 mMHEPPS11
82.5 mM11BeF3
95 mMglutamine11

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Data collection

DiffractionMean temperature: 120 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 17-ID / Synchrotron site: APS / Beamline: 17-ID / Wavelength: 1.2
DetectorType: BRUKER / Detector: CCD / Collection date: Nov 1, 1997
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 30 Å / Number obs: 700998 / Observed criterion sigma I: 0 / Rmerge I obs: 0.065 / Rsym value: 0.065 / NetI over sigmaI: 23.8 / Redundancy: 2.4 % / Percent possible obs: 92
Reflection shellRmerge I obs: 0.275 / Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / MeanI over sigI obs: 4 / Rsym value: 0.275 / Redundancy: 2 % / Percent possible all: 91
Reflection
*PLUS
Number measured all: 1676492
Reflection shell
*PLUS
Number unique obs: 85888 / Number measured obs: 170785 / Percent possible obs: 91

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
SAINT2000data reduction
XCALIBREdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JDB
Sigma F: 0 / Stereochemistry target values: TNT PROTGEO
Solvent computationSolvent model details: TNT / Solvent model param bsol: 290.8 / Solvent model param ksol: 0.99
Least-squares processR factor all: 0.191 / Highest resolution: 1.8 Å / Lowest resolution: 3 Å / Number reflection all: 700998 / Number reflection obs: 700998 / Percent reflection obs: 92
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 44248 / Nucleic acid: 0 / Ligand: 435 / Solvent: 4528 / Total: 49211
Refine LS restraints
Refine IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.014454676.000
X-RAY DIFFRACTIONt_angle_deg2.526130710.000
X-RAY DIFFRACTIONt_dihedral_angle_d17.7274210.000
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008122918.000
X-RAY DIFFRACTIONt_gen_planes0.01657950.000
X-RAY DIFFRACTIONt_it0493100.0
X-RAY DIFFRACTIONt_nbd0.032367
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.70.000
X-RAY DIFFRACTIONt_planar_d0.00818.000
X-RAY DIFFRACTIONt_plane_restr0.0150.000

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