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- PDB-3ou9: Crystal structure of gamma-carbonic anhydrase W19F mutant from Me... -

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Basic information

Entry
Database: PDB / ID: 3ou9
TitleCrystal structure of gamma-carbonic anhydrase W19F mutant from Methanosarcina thermophila
ComponentsCarbonic anhydrase
KeywordsLYASE / Cam / left-handed beta helix / ligands to zinc / trimer / bicarbonate.
Function / homology
Function and homology information


bicarbonate binding / sulfate binding / cobalt ion binding / carbonic anhydrase / carbonate dehydratase activity / extracellular region / zinc ion binding
Similarity search - Function
: / : / : / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
BICARBONATE ION / Carbonic anhydrase
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDomsic, J.F. / Robbins, A.H. / McKenna, R.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of gamma-carbonic anhydrase W19F mutant from Methanosarcina thermophila
Authors: Domsic, J.F. / Robbins, A.H. / McKenna, R.
History
DepositionSep 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9763
Polymers22,8491
Non-polymers1262
Water88349
1
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9279
Polymers68,5483
Non-polymers3796
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8020 Å2
ΔGint-140 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.582, 83.582, 83.582
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Carbonic anhydrase / gamma-carbonic anhydrase


Mass: 22849.221 Da / Num. of mol.: 1 / Fragment: UNP residues 35-247 / Mutation: W19F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina thermophila (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P40881, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG 8000 with 250 mM ammonium sulfate., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: mirror
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 18323 / Num. obs: 18298 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.064 / Χ2: 1.068 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.865.40.48417930.998199.9
1.86-1.945.40.34618371.0161100
1.94-2.035.50.22818011.004199.9
2.03-2.135.50.18418031.042199.9
2.13-2.275.50.12318321.073199.9
2.27-2.445.60.10418071.051100
2.44-2.695.80.08418371.0361100
2.69-3.075.90.05918371.1131100
3.07-3.875.90.0418551.137199.9
3.87-205.70.03819211.189199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.175 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.9143 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 926 5.06 %random
Rwork0.1346 ---
obs0.1359 18298 99.89 %-
all-18323 --
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.988 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 168.92 Å2 / Biso mean: 32.1975 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 5 49 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131650
X-RAY DIFFRACTIONf_angle_d1.4362272
X-RAY DIFFRACTIONf_chiral_restr0.108257
X-RAY DIFFRACTIONf_plane_restr0.008309
X-RAY DIFFRACTIONf_dihedral_angle_d11.93610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.89490.19381320.176124682600
1.8949-2.01350.18091120.136624412553
2.0135-2.16880.15231470.128524362583
2.1688-2.38660.17791500.125124532603
2.3866-2.73110.17231250.141524902615
2.7311-3.43770.16721340.138624922626
3.4377-19.17610.13921260.127725922718
Refinement TLS params.Method: refined / Origin x: 14.9889 Å / Origin y: -4.2559 Å / Origin z: -3.2009 Å
111213212223313233
T0.1122 Å20.0203 Å20.025 Å2-0.0996 Å2-0.0178 Å2--0.1247 Å2
L1.054 °20.2311 °2-0.1119 °2-1.0068 °2-0.2426 °2--1.527 °2
S-0.0399 Å °0.0469 Å °-0.1243 Å °-0.0985 Å °-0.0112 Å °-0.1585 Å °0.2235 Å °0.156 Å °0.0407 Å °
Refinement TLS groupSelection details: chain A and not element H

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