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- PDB-1bxr: STRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE COMPLEXED WITH THE AT... -

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Basic information

Entry
Database: PDB / ID: 1bxr
TitleSTRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE COMPLEXED WITH THE ATP ANALOG AMPPNP
Components(CARBAMOYL-PHOSPHATE ...) x 2
KeywordsAMIDOTRANSFERASE / CARBAMOYL-PHOSPHATE SYNTHASE
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / glutaminase activity / L-arginine biosynthetic process / glutamine metabolic process / amino acid binding ...carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / 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 / cytosol / cytoplasm
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 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glucose Oxidase; domain 1 / Rossmann fold - #20 / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / : / TETRAETHYLAMMONIUM ION / L-ornithine / Carbamoyl phosphate synthase large chain / Carbamoyl phosphate synthase small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsThoden, J.B. / Wesenberg, G. / Raushel, F.M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1999
Title: Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding.
Authors: Thoden, J.B. / Wesenberg, G. / Raushel, F.M. / Holden, H.M.
History
DepositionOct 8, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBAMOYL-PHOSPHATE SYNTHASE
B: CARBAMOYL-PHOSPHATE SYNTHASE
C: CARBAMOYL-PHOSPHATE SYNTHASE
D: CARBAMOYL-PHOSPHATE SYNTHASE
E: CARBAMOYL-PHOSPHATE SYNTHASE
F: CARBAMOYL-PHOSPHATE SYNTHASE
G: CARBAMOYL-PHOSPHATE SYNTHASE
H: CARBAMOYL-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)644,90370
Polymers637,8518
Non-polymers7,05362
Water58,4053242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: CARBAMOYL-PHOSPHATE SYNTHASE
F: CARBAMOYL-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,16916
Polymers159,4632
Non-polymers1,70614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-62 kcal/mol
Surface area46560 Å2
MethodPISA, PQS
3
C: CARBAMOYL-PHOSPHATE SYNTHASE
D: CARBAMOYL-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,29519
Polymers159,4632
Non-polymers1,83217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-81 kcal/mol
Surface area46180 Å2
MethodPISA, PQS
4
A: CARBAMOYL-PHOSPHATE SYNTHASE
B: CARBAMOYL-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,20017
Polymers159,4632
Non-polymers1,73815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-75 kcal/mol
Surface area46500 Å2
MethodPISA, PQS
5
G: CARBAMOYL-PHOSPHATE SYNTHASE
H: CARBAMOYL-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,24018
Polymers159,4632
Non-polymers1,77716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-71 kcal/mol
Surface area46530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.900, 164.500, 332.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein
CARBAMOYL-PHOSPHATE SYNTHASE


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


Mass: 41480.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6F1, carbamoyl-phosphate synthase (glutamine-hydrolysing)

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Non-polymers , 7 types, 3304 molecules

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


Mass: 54.938 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#7: Chemical
ChemComp-ORN / L-ornithine


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


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


Mass: 18.015 Da / Num. of mol.: 3242 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-IDChemical formula
1Mtetraethylammonium chloride11
2%(w/v)PEG800011
5mML-ornithine11
6mMAMPPNP11
7mMHEPPS11
8mg/mlprotein11
3mM11KCl
4mM11MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 446040 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.052 / Net I/σ(I): 29.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.265 / % possible all: 80
Reflection
*PLUS
Num. measured all: 1657168 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 80 % / Rmerge(I) obs: 0.265

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Processing

Software
NameVersionClassification
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: PDB ENTRY 1A9X

1a9x


Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: RESIDUES MODELED IN DUAL CONFORMATIONS: ASP A 757, MET A MET A 772, LYS A 881, ARG A 912, ARG E 104, ASN E 936, GLU E 1009, ARG G 490, AND ASN G 936
RfactorNum. reflection% reflection
Rwork0.195 --
all0.195 446040 -
obs-446040 93 %
Solvent computationBsol: 435.5 Å2 / ksol: 0.9 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44652 0 366 3242 48260
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.014579910
X-RAY DIFFRACTIONt_angle_deg2.1236179518
X-RAY DIFFRACTIONt_dihedral_angle_d18.31276710
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.007121225.5
X-RAY DIFFRACTIONt_gen_planes0.012665950
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.025813
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.12
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.30
X-RAY DIFFRACTIONt_plane_restr0.007

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