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- PDB-3r1w: Crystal structure of a carbonic anhydrase from a crude oil degrad... -

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Basic information

Entry
Database: PDB / ID: 3r1w
TitleCrystal structure of a carbonic anhydrase from a crude oil degrading psychrophilic library
Componentscarbonic anhydrase
KeywordsLYASE / BETA-HELIX / CARBONIC ANHYDRASE
Function / homologyHexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Mainly Beta
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPetit, P. / Xu, X. / Cui, H. / Brown, G. / Dong, A. / Savchenko, A. / Yakunin, A.F.
CitationJournal: To be Published
Title: Crystal structure of a carbonic anhydrase from a crude oil degrading psychrophilic library
Authors: Petit, P. / Xu, X. / Cui, H. / Brown, G. / Dong, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionMar 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: carbonic anhydrase
B: carbonic anhydrase
C: carbonic anhydrase


Theoretical massNumber of molelcules
Total (without water)61,4203
Polymers61,4203
Non-polymers00
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-35 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.071, 89.943, 54.720
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein carbonic anhydrase


Mass: 20473.432 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others)
Description: Isolated from a crude oil degrading psychrophilic library
Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M tri-NaCitrate, 0.2M NaCl, 25%PEG3350. 1/70 Trypsin, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 23, 2006 / Details: MSC/Yale double focusing mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.73→36.96 Å / Num. obs: 50561 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.047 / Rsym value: 0.044 / Net I/σ(I): 33.2
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 10 / Num. unique all: 6497 / Rsym value: 0.189 / % possible all: 83.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1V67

1v67


Resolution: 1.73→34.657 Å / SU ML: 0.19 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1894 2539 5.07 %RANDOM
Rwork0.1574 ---
obs0.159 50098 92.72 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.333 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8549 Å20 Å2-0.2731 Å2
2--1.4808 Å2-0 Å2
3---0.3741 Å2
Refinement stepCycle: LAST / Resolution: 1.73→34.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4071 0 0 462 4533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074151
X-RAY DIFFRACTIONf_angle_d1.1065629
X-RAY DIFFRACTIONf_dihedral_angle_d11.5771495
X-RAY DIFFRACTIONf_chiral_restr0.075644
X-RAY DIFFRACTIONf_plane_restr0.004728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.76550.2445920.18881909X-RAY DIFFRACTION67
1.7655-1.80160.27681380.18162521X-RAY DIFFRACTION89
1.8016-1.84080.21251340.17582539X-RAY DIFFRACTION90
1.8408-1.88360.21051260.15542611X-RAY DIFFRACTION91
1.8836-1.93070.19941290.14952593X-RAY DIFFRACTION91
1.9307-1.98290.19771440.14842601X-RAY DIFFRACTION92
1.9829-2.04120.20351430.14612627X-RAY DIFFRACTION93
2.0412-2.10710.19671690.15422648X-RAY DIFFRACTION94
2.1071-2.18240.19031170.14952696X-RAY DIFFRACTION94
2.1824-2.26980.18731410.15422677X-RAY DIFFRACTION94
2.2698-2.3730.18871500.15562689X-RAY DIFFRACTION94
2.373-2.49810.19451710.15652695X-RAY DIFFRACTION96
2.4981-2.65460.21651370.17042700X-RAY DIFFRACTION96
2.6546-2.85940.18351670.17362750X-RAY DIFFRACTION97
2.8594-3.1470.19981440.16742794X-RAY DIFFRACTION97
3.147-3.6020.19731470.15922808X-RAY DIFFRACTION97
3.602-4.53650.14091620.12962802X-RAY DIFFRACTION98
4.5365-34.66350.15821280.16512899X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.4447 Å / Origin y: 39.8277 Å / Origin z: 49.1009 Å
111213212223313233
T0.0123 Å20.0058 Å2-0.0014 Å2-0.0177 Å2-0.0076 Å2--0.0134 Å2
L0.0316 °2-0.0308 °2-0.0189 °2-0.0546 °20.0038 °2--0.0322 °2
S-0.0086 Å °-0.0086 Å °0.0052 Å °0.0053 Å °0.0072 Å °-0.0103 Å °0.0003 Å °-0.0049 Å °0.0011 Å °
Refinement TLS groupSelection details: all

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