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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: 1e19
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 / homologyCarbamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / carbamate kinase / carbamate kinase activity / arginine metabolic process / ATP binding / cytoplasm / Carbamate kinase
Function and homology information
Specimen sourcePYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.5 Å resolution
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 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 28, 2000 / Release: Jul 4, 2000
RevisionDateData content typeGroupProviderType
1.0Jul 4, 2000Structure modelrepositoryInitial release
1.1May 30, 2012Structure modelDatabase references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,8546
Polyers68,9512
Non-polymers9034
Water12,899716
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6540
ΔGint (kcal/M)-57.4
Surface area (Å2)25050
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 21

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Components

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


Mass: 34475.582 Da / Num. of mol.: 2 / 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 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.5 / Density percent 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
Temp: 22 ℃ / Method: vapor diffusion, hanging drop / pH: 8.5
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
150 mMTris-HCldrop
220 mMATPdrop
320 mMdropMgCl2
41.3 Msodium citratereservoir
50.1 MTris-HClreservoirpH8.5

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: ESRF / Synchrotron site: ESRF / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Sep 15, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionD resolution high: 1.43 Å / D resolution low: 76.67 Å / Number obs: 116569 / Rmerge I obs: 0.067 / Rsym value: 0.067 / NetI over sigmaI: 5.2 / Redundancy: 3.8 % / Percent possible obs: 97.3
Reflection shellRmerge I obs: 0.355 / Highest resolution: 1.5 Å / Lowest resolution: 1.59 Å / MeanI over sigI obs: 1.9 / Rsym value: 0.355 / Percent possible all: 98.6
Reflection
*PLUS
Number measured all: 448640
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Percent possible obs: 98.6

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B7B
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.218 / R factor R work: 0.183 / Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Number reflection R free: 6517 / Number reflection obs: 101284 / Percent reflection R free: 6 / Percent reflection obs: 97
Refine hist #LASTHighest resolution: 1.5 Å / Lowest resolution: 15 Å
Number of atoms included #LASTProtein: 4826 / Nucleic acid: 0 / Ligand: 56 / Solvent: 716 / Total: 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
Least-squares process
*PLUS
R factor obs: 0.183
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg9.9
Refine LS shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.66 Å / Number reflection obs: 24677 / Number reflection R free: 1593 / R factor obs: 0.229 / R factor R free: 0.267

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