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- PDB-1qrf: A CLOSER LOOK AT THE ACTIVE SITE OF GAMMA-CARBONIC ANHYDRASES: HI... -

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Basic information

Entry
Database: PDB / ID: 1qrf
TitleA CLOSER LOOK AT THE ACTIVE SITE OF GAMMA-CARBONIC ANHYDRASES: HIGH RESOLUTION CRYSTALLOGRAPHIC STUDIES OF THE CARBONIC ANHYDRASE FROM METHANOSARCINA THERMOPHILA
ComponentsCARBONIC ANHYDRASE
KeywordsLYASE / BETA-HELIX
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
: / Carbonic anhydrase
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.55 Å
AuthorsIverson, T.M. / Alber, B.E. / Kisker, C. / Ferry, J.G. / Rees, D.C.
Citation
Journal: Biochemistry / Year: 2000
Title: A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila.
Authors: Iverson, T.M. / Alber, B.E. / Kisker, C. / Ferry, J.G. / Rees, D.C.
#1: Journal: Embo J. / Year: 1996
Title: A Left-Handed Beta-Helix Revealed by the Crystal Structure of a Carbonic Anhydrase from the Archaeon Methanosarcina thermophila
Authors: Kisker, C. / Schindelin, H. / Alber, B. / Ferry, J. / Rees, D.
History
DepositionJun 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)23,0433
Polymers22,8881
Non-polymers1552
Water1,53185
1
A: CARBONIC ANHYDRASE
hetero molecules

A: CARBONIC ANHYDRASE
hetero molecules

A: CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1309
Polymers68,6653
Non-polymers4656
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 area8670 Å2
ΔGint-129 kcal/mol
Surface area20700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.608, 82.608, 82.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein CARBONIC ANHYDRASE


Mass: 22888.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina thermophila (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P40881
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 8000, ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
25 mMphosphate1drop
35 %PEG80001reservoir
40.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 19, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. all: 27562 / Num. obs: 25247 / % possible obs: 91.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3 % / Rmerge(I) obs: 0.276 / % possible all: 90.3
Reflection
*PLUS
% possible obs: 91.5 % / Num. measured all: 91423
Reflection shell
*PLUS
% possible obs: 90.3 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 1.55→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: refmac
RfactorNum. reflectionSelection details
Rfree0.229 1028 random
Rwork0.205 --
all0.21 27562 -
obs0.21 25247 -
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 6 85 1628
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_deg1.7
X-RAY DIFFRACTIONp_bond_d0.014

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