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- PDB-5hpj: Photobacterium profundum alpha-carbonic anhydrase -

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Basic information

Entry
Database: PDB / ID: 5hpj
TitlePhotobacterium profundum alpha-carbonic anhydrase
ComponentsCarbonic anhydrase
KeywordsLYASE / carbonic anhydrase / psychrophile / alpha class
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. ...Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesPhotobacterium profundum SS9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSomalinga, V. / Buhrman, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1332341 United States
CitationJournal: PLoS ONE / Year: 2016
Title: A High-Resolution Crystal Structure of a Psychrohalophilic alpha-Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface.
Authors: Somalinga, V. / Buhrman, G. / Arun, A. / Rose, R.B. / Grunden, A.M.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3233
Polymers24,2221
Non-polymers1012
Water6,161342
1
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6466
Polymers48,4442
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1950 Å2
ΔGint-96 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.461, 60.461, 95.464
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-302-

CL

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Components

#1: Protein Carbonic anhydrase


Mass: 24221.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium profundum SS9 (bacteria)
Strain: SS9 / Gene: EBIG1812, PBPRA3376 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6LM17
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2015
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 33011 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 11.82 Å2 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.115 / Rrim(I) all: 0.256 / Χ2: 1.302 / Net I/av σ(I): 23.707 / Net I/σ(I): 6.8 / Num. measured all: 260731
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.5-1.536.416340.4080.850.756100
1.53-1.556.516200.5590.6430.806100
1.55-1.586.716220.6860.6410.829100
1.58-1.626.916170.8360.540.867100
1.62-1.657.116330.8060.5650.858100
1.65-1.697.316350.8250.5050.873100
1.69-1.737.516310.7340.5120.916100
1.73-1.787.716300.8360.440.992100
1.78-1.837.716360.9070.3931.104100
1.83-1.897.916300.9680.3231.1471000.8460.906
1.89-1.968.116240.970.2691.2711000.7210.771
1.96-2.048.216350.9690.2121.2951000.5730.611
2.04-2.138.416530.9790.1931.4641000.5320.566
2.13-2.248.816480.9830.181.5071000.5140.545
2.24-2.388.716500.9810.1581.5971000.4470.475
2.38-2.568.816660.9920.1261.5711000.3630.385
2.56-2.828.816670.9930.0931.7221000.270.286
2.82-3.238.916670.9960.0631.7671000.1840.195
3.23-4.078.817170.9970.0381.9411000.110.116
4.07-508.317960.9980.031.899.60.0860.091

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3T

4c3t


Resolution: 1.5→28.82 Å / FOM work R set: 0.9067 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 2006 6.08 %Random
Rwork0.1389 30963 --
obs0.1406 32969 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.69 Å2 / Biso mean: 16.09 Å2 / Biso min: 6.06 Å2
Refinement stepCycle: final / Resolution: 1.5→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 2 342 2051
Biso mean--10.39 24.97 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091768
X-RAY DIFFRACTIONf_angle_d1.3582413
X-RAY DIFFRACTIONf_chiral_restr0.076268
X-RAY DIFFRACTIONf_plane_restr0.007321
X-RAY DIFFRACTIONf_dihedral_angle_d14.25649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5003-1.53780.2681410.199621952336
1.5378-1.57940.22891380.172421612299
1.5794-1.62590.19421450.165521702315
1.6259-1.67830.21141450.155122032348
1.6783-1.73830.19561420.154721782320
1.7383-1.80790.17531410.14321622303
1.8079-1.89020.18241400.13622162356
1.8902-1.98980.16491410.131821732314
1.9898-2.11440.17441430.131422262369
2.1144-2.27760.16841370.130722042341
2.2776-2.50670.16381450.130322212366
2.5067-2.86920.16651440.134522312375
2.8692-3.61370.14441460.132122602406
3.6137-28.82530.14381580.134523632521

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