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- PDB-1ce8: CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1ce8
TitleCARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEXED WITH THE ALLOSTERIC LIGAND IMP
Components(PROTEIN (CARBAMOYL-PHOSPHATE ...) x 2
KeywordsLIGASE IMP / IMP / ALLOSTERIC LIGAND
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
ADENOSINE-5'-DIPHOSPHATE / INOSINIC ACID / : / : / TETRAETHYLAMMONIUM ION / L-ornithine / PHOSPHATE ION / 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. / Raushel, F.M. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase.
Authors: Thoden, J.B. / Raushel, F.M. / Wesenberg, G. / Holden, H.M.
History
DepositionMar 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)646,80288
Polymers637,8548
Non-polymers8,94880
Water72,7274037
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
B: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polymers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-60 kcal/mol
Surface area46890 Å2
MethodPISA, PQS
3
G: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
H: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polymers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-60 kcal/mol
Surface area46830 Å2
MethodPISA, PQS
4
C: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
D: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polymers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-57 kcal/mol
Surface area47010 Å2
MethodPISA, PQS
5
E: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
F: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polymers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-55 kcal/mol
Surface area46570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.100, 163.900, 331.200
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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PROTEIN (CARBAMOYL-PHOSPHATE ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)


Mass: 117982.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LONG CHAIN / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein
PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)


Mass: 41480.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SHORT CHAIN / 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 , 9 types, 4117 molecules

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


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


Mass: 39.098 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: 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
#8: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H12N2O2
#9: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#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.: 4037 / 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
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.65 Mtetraethylammonium chloride11
28 %(w/v)PEG800011
3100 mM11KCl
40.5 mM11MnCl2
50.5 mMornithine11
61.25 mMADP11
71.25 mMBeF311
85.0 mMIMP11
925 mMHEPES11

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 445013 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 30.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.221 / % possible all: 81
Reflection shell
*PLUS
% possible obs: 81 % / Num. unique obs: 38417

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A9X

1a9x


Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: MISSING RESIDUES THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST ...Details: MISSING RESIDUES THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2225 5 %RANDOM
Rwork0.193 ---
all0.193 445013 --
obs0.192 445013 93 %-
Solvent computationSolvent model: TNT / Bsol: 403.8 Å2 / ksol: 0.881 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44220 0 488 4037 48745
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.013455637.5
X-RAY DIFFRACTIONt_angle_deg2.36144613
X-RAY DIFFRACTIONt_dihedral_angle_d17.899274560
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005122440
X-RAY DIFFRACTIONt_gen_planes0.009660565
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.04796
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 22250 / Rfactor all: 0.192 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.8990
X-RAY DIFFRACTIONt_planar_d0.00540
X-RAY DIFFRACTIONt_plane_restr0.00965

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