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- PDB-1e19: Structure of the carbamate kinase-like carbamoyl phosphate synthe... -

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Basic information

Entry
Database: PDB / ID: 1.0E+19
TitleStructure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus bound to ADP
ComponentsCARBAMATE KINASE
KeywordsTRANSFERASE / HYPERTHERMOPHILES / ADP SITE / ARGININE METABOLISM PHOSPHORYL GROUP TRANSFER
Function / homology
Function and homology information


carbamate kinase / carbamate kinase activity / L-arginine deiminase pathway / ATP binding / cytosol
Similarity search - Function
Carbamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Carbamate kinase
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRamon-Maiques, S. / Marina, A. / Uriarte, M. / Fita, I. / Rubio, V.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The 1.5-A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This ...Title: The 1.5-A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This Thermoestable Enzyme is a Carbamate Kinase, and Provides Insights Into Substrate Binding and Stability in Carbamate Kinases
Authors: Ramon-Maiques, S. / Marina, A. / Uriarte, M. / Fita, I. / Rubio, V.
History
DepositionApr 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBAMATE KINASE
B: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8546
Polymers68,9512
Non-polymers9034
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-57.4 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.400, 91.700, 133.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.958996, -0.047676, 0.279105), (-0.045924, -0.998832, -0.012663), (0.279287, -0.000725, -0.960184)
Vector: -7.73523, 70.02999, 66.25964)

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Components

#1: Protein CARBAMATE KINASE / CARBAMATE KINASE-LIKE CARBAMOYLPHOSPHATE SYNTETASE / CARBAMATE KINASE-LIKE CARBAMOYLPHOSPHATE SYNTHASE


Mass: 34475.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PYROCOCCUS FURIOSUS (archaea) / References: UniProt: P95474, carbamate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 8
Details: 1.3M SODIUM CITRATE 0.1M TRIS-HCL, PH=8.5, 0-10% ETHYLENE GLYCOL PROTEIN SOLUTION: 10MG/ML OF PROTEIN IN 10MM TRIS-HCL CONTAINING 20MM ATP AND MGCL2, pH 8.00
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mMTris-HCl1drop
220 mMATP1drop
320 mM1dropMgCl2
41.3 Msodium citrate1reservoir
50.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.43→76.67 Å / Num. obs: 116569 / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 5.2
Reflection shellResolution: 1.5→1.59 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.355 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 448640
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 98.6 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B7B

1b7b


Resolution: 1.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6517 6 %RANDOM
Rwork0.183 ---
obs-101284 97 %-
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 56 716 5598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg9.9
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.66 Å / Rfactor Rfree: 0.267 / Num. reflection Rfree: 1593 / Num. reflection obs: 24677 / Rfactor obs: 0.229

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