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- PDB-1c3o: CRYSTAL STRUCTURE OF THE CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SU... -

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Basic information

Entry
Database: PDB / ID: 1c3o
TitleCRYSTAL STRUCTURE OF THE CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT MUTANT C269S WITH BOUND GLUTAMINE
Components(CARBAMOYL PHOSPHATE SYNTHETASE: ...) x 2
KeywordsLIGASE / AMIDOTRANSFERASE / MICHAELIS COMPLEX / ATP-GRASP
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 / 2.1 Å resolution
AuthorsThoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1999
Title: The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway.
Authors: Thoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 28, 1999 / Release: Dec 10, 1999
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 10, 1999Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)646,37997
Polyers637,7908
Non-polymers8,58989
Water66,0433666
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)152.500, 164.400, 332.600
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 SUBUNIT


Mass: 117981.750 Da / Num. of mol.: 4 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Production host: Bacteria (eubacteria)
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein/peptide
CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT


Mass: 41465.816 Da / Num. of mol.: 4 / Mutation: C269S / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Production host: Bacteria (eubacteria)
References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing)

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Non-polymers , 9 types, 3755 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 35.453 Da / Num. of mol.: 16 / Formula: Cl / Chloride
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Formula: PO4 / Phosphate
#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-GLN / GLUTAMINE


Mass: 146.144 Da / Num. of mol.: 8 / Formula: C5H10N2O3 / Glutamine
#10: Chemical
ChemComp-NET / TETRAETHYLAMMONIUM ION


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


Mass: 18.015 Da / Num. of mol.: 3666 / 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: 3.27 / Density percent sol: 62.35 %
Crystal growTemp: 278 K / Method: batch / pH: 7.4
Details: PEG-8000, MANGANESE CHLORIDE, TETRAETHYLAMMONIUM CHLORIDE, POTASSIUM CHLORIDE, BERYLLIUM FLUORIDE, ADENOSINE 5'-DIPHOSPHATE,L-ORNITHINE, L-GLUTAMINE, HEPPS, pH 7.4, BATCH, temperature 278K
Crystal grow
*PLUS
Temp: 4 ℃ / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
18 %PEG800011
20.65 Mtetraethylammonium chloride11
30.5 mM11MnCl2
4100 mM11KCl
51.5 mMADP11
61.5 mM11BeF3
70.5 mML-ornithine11
825 mMHEPPS11

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 19-ID / Synchrotron site: APS / Beamline: 19-ID / Wavelength: 0.7005
DetectorType: CUSTOM-MADE / Detector: CCD / Collection date: Feb 24, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7005 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 3 Å / Number all: 476527 / Number obs: 476527 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.079 / NetI over sigmaI: 16.6 / Redundancy: 5.3 % / Percent possible obs: 98.4
Reflection shellRmerge I obs: 0.282 / Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / Redundancy: 4.3 % / Percent possible all: 97.9
Reflection
*PLUS
Number measured all: 2532077
Reflection shell
*PLUS
Number unique obs: 47060 / Number measured obs: 201948 / Percent possible obs: 97.9 / MeanI over sigI obs: 2.2

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
d*TREKdata reduction
HKL-2000data scaling
RefineR Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: ENGH & HUBER
Least-squares processR factor R free: 0.258 / R factor R work: 0.188 / R factor all: 0.189 / R factor obs: 0.189 / Highest resolution: 2.1 Å / Lowest resolution: 3 Å / Number reflection R free: 49936 / Number reflection all: 476527 / Number reflection obs: 476527 / Percent reflection obs: 98.4
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 44220 / Nucleic acid: 0 / Ligand: 453 / Solvent: 3666 / Total: 48339
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg2.19
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
R factor all: 0.189
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.190
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.011

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