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- PDB-1jdb: CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1jdb
TitleCARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIA COLI
Components(CARBAMOYL PHOSPHATE ...) x 2
KeywordsLIGASE / AMIDOTRANSFERASE / SYNTHASE
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / glutaminase activity / L-arginine biosynthetic process / glutamine metabolic process ...carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / glutaminase activity / L-arginine biosynthetic process / glutamine metabolic process / amino acid binding / amino acid biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein heterodimerization activity / nucleotide binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation 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 small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation 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 / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Glucose Oxidase; domain 1 / Rossmann fold - #20 / Glutamine amidotransferase / Glutamine amidotransferase class-I / 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, A domain / Class I glutamine amidotransferase (GATase) domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 3-Layer(bba) Sandwich / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GLUTAMINE / : / : / TETRAETHYLAMMONIUM ION / L-ornithine / PHOSPHATE ION / Carbamoyl-phosphate synthase small chain / Carbamoyl phosphate synthase large chain / Carbamoyl phosphate synthase small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsThoden, J.B. / Holden, H.M. / Wesenberg, G. / Raushel, F.M. / Rayment, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.
Authors: Thoden, J.B. / Raushel, F.M. / Benning, M.M. / Rayment, I. / Holden, H.M.
#1: Journal: Biochemistry / Year: 1997
Title: Structure of Carbamoyl Phosphate Synthetase: A Journey of 96 a from Substrate to Product
Authors: Thoden, J.B. / Holden, H.M. / Wesenberg, G. / Raushel, F.M. / Rayment, I.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CARBAMOYL PHOSPHATE SYNTHETASE
C: CARBAMOYL PHOSPHATE SYNTHETASE
E: CARBAMOYL PHOSPHATE SYNTHETASE
F: CARBAMOYL PHOSPHATE SYNTHETASE
H: CARBAMOYL PHOSPHATE SYNTHETASE
I: CARBAMOYL PHOSPHATE SYNTHETASE
K: CARBAMOYL PHOSPHATE SYNTHETASE
L: CARBAMOYL PHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,383115
Polymers637,8518
Non-polymers9,532107
Water87,4994857
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CARBAMOYL PHOSPHATE SYNTHETASE
C: CARBAMOYL PHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,80328
Polymers159,4632
Non-polymers2,34126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-80 kcal/mol
Surface area47300 Å2
MethodPISA, PQS
3
H: CARBAMOYL PHOSPHATE SYNTHETASE
I: CARBAMOYL PHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,76427
Polymers159,4632
Non-polymers2,30225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-80 kcal/mol
Surface area47580 Å2
MethodPISA, PQS
4
K: CARBAMOYL PHOSPHATE SYNTHETASE
L: CARBAMOYL PHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,93730
Polymers159,4632
Non-polymers2,47528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-82 kcal/mol
Surface area47650 Å2
MethodPISA, PQS
5
E: CARBAMOYL PHOSPHATE SYNTHETASE
F: CARBAMOYL PHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,87830
Polymers159,4632
Non-polymers2,41528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-78 kcal/mol
Surface area47020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.800, 167.700, 323.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99134, -0.001972, 0.131303), (-0.003915, -0.999887, 0.014538), (0.13126, -0.014926, -0.991236)0.55268, 95.47849, 15.74338
2given(-0.989687, 0.042261, -0.136871), (0.112782, -0.35921, -0.926417), (-0.088317, -0.932299, 0.350739)108.71375, 69.4916, 57.1515
3given(-0.99754, 0.019513, -0.067328), (-0.055814, 0.360007, 0.931279), (0.042411, 0.932746, -0.358032)111.11224, 22.74961, -31.90683
4given(0.991231, -0.029949, 0.128703), (-0.028363, -0.999498, -0.014133), (0.129062, 0.010359, -0.991582)3.10394, 94.83478, 13.90623
5given(-0.984436, 0.142048, -0.103478), (0.052375, -0.324916, -0.944292), (-0.167757, -0.935014, 0.312419)103.51321, 68.61298, 58.95157
6given(-0.994737, 0.061789, -0.081734), (-0.058385, 0.313703, 0.947725), (0.084199, 0.947509, -0.308444)105.95749, 27.77397, -31.96624

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Components

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CARBAMOYL PHOSPHATE ... , 2 types, 8 molecules BEHKCFIL

#1: Protein
CARBAMOYL PHOSPHATE SYNTHETASE


Mass: 117981.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein
CARBAMOYL PHOSPHATE SYNTHETASE


Mass: 41480.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing)

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Non-polymers , 9 types, 4964 molecules

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


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#4: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#6: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H10N2O3
#8: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2
#10: Chemical
ChemComp-NET / TETRAETHYLAMMONIUM ION


Mass: 130.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H20N
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4857 / 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 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.4
Details: 0.65M TETRAETHYL AMMONIUM CHLORIDE (E4NCL) 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM HEPES PH 7.4. THE CRYSTAL WAS SOAKED INTO: 1.4M E4NCL 8% PEG 8000 250MM KCL 2.5MM ...Details: 0.65M TETRAETHYL AMMONIUM CHLORIDE (E4NCL) 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM HEPES PH 7.4. THE CRYSTAL WAS SOAKED INTO: 1.4M E4NCL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL.
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common 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

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 404724 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 22.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.203 / % possible all: 73
Reflection shell
*PLUS
% possible obs: 73 % / Num. unique obs: 32559

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JDB

1jdb


Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.179 --
all-404724 -
obs-404724 90 %
Solvent computationSolvent model: TNT / Bsol: 556 Å2 / ksol: 1.027 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44220 0 487 4857 49564
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.011455698.5
X-RAY DIFFRACTIONt_angle_deg2.616143010
X-RAY DIFFRACTIONt_dihedral_angle_d17.6274700
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004122240
X-RAY DIFFRACTIONt_gen_planes0.009660270
X-RAY DIFFRACTIONt_it500497360
X-RAY DIFFRACTIONt_nbd0.034805
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.60
X-RAY DIFFRACTIONt_plane_restr0.0970

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