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- PDB-8crv: Crystal Structure of the Carbamate Kinase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 8crv
TitleCrystal Structure of the Carbamate Kinase from Pseudomonas aeruginosa
ComponentsCarbamate kinase
KeywordsTRANSFERASE / Carbamate Kinase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


carbamate kinase / carbamate kinase activity / L-arginine deiminase pathway / ATP binding / cytosol
Similarity search - Function
Carbamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family
Similarity search - Domain/homology
FORMIC ACID / oxidanyl dihydrogen phosphate / Carbamate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKim, Y. / Skarina, T. / Mesa, N. / Stogios, P. / Savchenko, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Carbamate Kinase from Pseudomonas aeruginosa
Authors: Kim, Y. / Skarina, T. / Mesa, N. / Stogios, P. / Savchenko, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 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
A: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1229
Polymers33,4191
Non-polymers7028
Water4,882271
1
A: Carbamate kinase
hetero molecules

A: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,24318
Polymers66,8392
Non-polymers1,40516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6670 Å2
ΔGint-132 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.560, 56.560, 250.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-724-

HOH

31A-728-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbamate kinase


Mass: 33419.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: arcC, PA5173 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13982, carbamate kinase

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Non-polymers , 5 types, 279 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-OO9 / oxidanyl dihydrogen phosphate


Mass: 113.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O5P
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 58.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 0.1 M Hepes pH 7.5, 2 %(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→46.82 Å / Num. obs: 55145 / % possible obs: 99.9 % / Redundancy: 19.1 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.022 / Rrim(I) all: 0.1 / Net I/σ(I): 18.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2654 / CC1/2: 0.623 / Rpim(I) all: 0.533 / Rrim(I) all: 1.566 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
xia2data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: swiss pro

Resolution: 1.6→39.99 Å / SU ML: 0.174 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.3603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1964 2755 5.01 %
Rwork0.1813 52239 -
obs0.1821 54994 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 38 271 2650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532528
X-RAY DIFFRACTIONf_angle_d0.80573442
X-RAY DIFFRACTIONf_chiral_restr0.0569382
X-RAY DIFFRACTIONf_plane_restr0.008459
X-RAY DIFFRACTIONf_dihedral_angle_d13.3769958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.33421280.33132519X-RAY DIFFRACTION98.77
1.63-1.660.28341480.27122529X-RAY DIFFRACTION99.7
1.66-1.690.30681320.25012557X-RAY DIFFRACTION99.96
1.69-1.720.22121080.21182574X-RAY DIFFRACTION99.93
1.72-1.760.2041280.19642597X-RAY DIFFRACTION99.96
1.76-1.80.18821250.1772557X-RAY DIFFRACTION100
1.8-1.850.21321280.17522580X-RAY DIFFRACTION99.89
1.85-1.90.19591280.18052607X-RAY DIFFRACTION99.93
1.9-1.950.20041320.18162594X-RAY DIFFRACTION99.96
1.95-2.020.20851390.17632580X-RAY DIFFRACTION99.93
2.02-2.090.20041110.17532598X-RAY DIFFRACTION99.93
2.09-2.170.19341420.16962598X-RAY DIFFRACTION99.93
2.17-2.270.16791410.17122583X-RAY DIFFRACTION99.89
2.27-2.390.19271620.17182579X-RAY DIFFRACTION99.96
2.39-2.540.23081470.17822609X-RAY DIFFRACTION100
2.54-2.740.2111440.19212638X-RAY DIFFRACTION99.96
2.74-3.010.22331440.19042648X-RAY DIFFRACTION100
3.01-3.450.20431380.19052675X-RAY DIFFRACTION100
3.45-4.340.14871450.16162744X-RAY DIFFRACTION100
4.34-39.990.19141850.17492873X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5495060589590.178610426879-0.1888114296430.618899981410.04811589129040.6642644023180.009040595892080.0673932214944-0.00261999455402-0.0549033732543-0.005809748254910.0824223801693-0.0198626328582-0.0549787880613-3.86443375765E-60.169501135585-0.000896338798781-0.02483110903380.1701249868020.01760175904670.172127214125-16.0217508177-6.45019992307-7.54542605642
20.353649149907-0.229670326249-0.05691868681360.339431884544-0.2034632253130.5095659497960.05920766569220.05603820161740.00631888655479-0.0533681909166-0.0716060975950.105682110508-0.0912386512199-0.0271134104665-8.95405255947E-60.2854323036730.00818771283099-0.02483552271580.1754717295450.01551915638570.212266033651-12.59701499323.93919961277-28.3571243899
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 217 )-1 - 2171 - 219
22chain 'A' and (resid 218 through 310 )218 - 310220 - 312

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