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- PDB-3ow5: Crystal structure of the Y200A mutant of gamma carbonic anhydrase... -

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Basic information

Entry
Database: PDB / ID: 3ow5
TitleCrystal structure of the Y200A mutant of gamma carbonic anhydrase from Methanosarcina thermophila
ComponentsCarbonic anhydrase
KeywordsLYASE / Cam / ligands to zinc / left-handed beta helix / trimer / sulfate / bicarbonate
Function / homology
Function and homology information


bicarbonate binding / sulfate binding / cobalt ion binding / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding / extracellular region
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: 1.801 Å
AuthorsDomsic, J.F. / Robbins, A.H. / McKenna, R.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the Y200A mutant of Methanosarcina thermophila
Authors: Domsic, J.F. / Robbins, A.H. / McKenna, R.
History
DepositionSep 17, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0745
Polymers22,7961
Non-polymers2784
Water1,20767
1
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22315
Polymers68,3883
Non-polymers83512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area8480 Å2
ΔGint-203 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.498, 83.498, 83.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-215-

FE

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbonic anhydrase / gamma carbonic anhydrase


Mass: 22796.162 Da / Num. of mol.: 1 / Fragment: UNP residues 35-247 / Mutation: Y200A
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

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Non-polymers , 5 types, 71 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 42.2 %
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→25 Å / Num. obs: 18286 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.045 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.866.20.34918241.061100
1.86-1.946.30.25517981.0691100
1.94-2.036.40.19318021.0871100
2.03-2.136.40.14817831.041100
2.13-2.276.50.118260.9581100
2.27-2.446.60.08818241.0331100
2.44-2.696.60.07418301.0381100
2.69-3.086.60.05118221.0221100
3.08-3.876.60.03318481.0411100
3.87-256.40.02719291.099199.9

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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: 1.801→24.104 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.923 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1517 923 5.06 %random
Rwork0.1285 ---
obs0.1296 18229 99.93 %-
all-18232 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.91 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 153.52 Å2 / Biso mean: 26.2503 Å2 / Biso min: 5.13 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.801→24.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 11 67 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191610
X-RAY DIFFRACTIONf_angle_d1.4262208
X-RAY DIFFRACTIONf_chiral_restr0.114253
X-RAY DIFFRACTIONf_plane_restr0.008298
X-RAY DIFFRACTIONf_dihedral_angle_d12.022588
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
1.8012-1.89610.18191290.156424462575
1.8961-2.01490.16981160.131324532569
2.0149-2.17030.15141440.120524372581
2.1703-2.38860.14111490.119624302579
2.3886-2.73380.1741270.13224712598
2.7338-3.44270.16121310.134524832614
3.4427-24.10590.12991270.122925862713
Refinement TLS params.Method: refined / Origin x: 17.5872 Å / Origin y: 58.4782 Å / Origin z: 47.7822 Å
111213212223313233
T0.0872 Å2-0.0169 Å2-0.0099 Å2-0.074 Å2-0.0099 Å2--0.0874 Å2
L1.1084 °2-0.1469 °20.1264 °2-0.6691 °2-0.1662 °2--0.736 °2
S0.0442 Å °0.1069 Å °-0.1794 Å °-0.1025 Å °-0.0147 Å °0.0692 Å °0.0891 Å °-0.0411 Å °-0.0296 Å °
Refinement TLS groupSelection details: chain A and not element H and not element FE

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