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- PDB-1thj: CARBONIC ANHYDRASE FROM METHANOSARCINA -

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Basic information

Entry
Database: PDB / ID: 1thj
TitleCARBONIC ANHYDRASE FROM METHANOSARCINA
ComponentsCARBONIC ANHYDRASE
KeywordsLYASE (OXO-ACID) / CARBONIC ANHYDRASE
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
Biological speciesMethanosarcina thermophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsKisker, C. / Schindelin, H. / Rees, D.C.
Citation
Journal: EMBO J. / Year: 1996
Title: A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila.
Authors: Kisker, C. / Schindelin, H. / Alber, B.E. / Ferry, J.G. / Rees, D.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: A Carbonic Anhydrase from the Archaeon Methanosarcina Thermophila
Authors: Alber, B.E. / Ferry, J.G.
History
DepositionApr 2, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / software / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_id / _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.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE
B: CARBONIC ANHYDRASE
C: CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2586
Polymers69,0613
Non-polymers1963
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-150 kcal/mol
Surface area23400 Å2
MethodPISA
2
A: CARBONIC ANHYDRASE
B: CARBONIC ANHYDRASE
C: CARBONIC ANHYDRASE
hetero molecules

A: CARBONIC ANHYDRASE
B: CARBONIC ANHYDRASE
C: CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,51512
Polymers138,1236
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area21320 Å2
ΔGint-323 kcal/mol
Surface area42440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.840, 71.840, 333.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.19073, 0.363911, 0.911696), (-0.972713, -0.195047, -0.12564), (0.132102, -0.910783, 0.391183)-117.8558, 110.468, 133.70509
2given(-0.194148, -0.971069, 0.13904), (0.36036, -0.202427, -0.910584), (0.912385, -0.126684, 0.389236)66.3651, 186.6181, 69.3735

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Components

#1: Protein CARBONIC ANHYDRASE / CAM


Mass: 23020.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: MET 0 IS DUE TO CLONING ARTIFACT / Source: (gene. exp.) Methanosarcina thermophila (archaea) / References: UniProt: P40881, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.11 Å3/Da / Density % sol: 60 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.0 Mammonium sulfate11
23 %PEG40011
30.1 Mcacodylate12
40.02 %12NaN3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionNum. obs: 21401 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Highest resolution: 2.8 Å
Reflection shell
*PLUS
% possible obs: 82.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.324

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementResolution: 2.8→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.295 -
Rwork0.234 -
obs0.234 20764
Displacement parametersBiso mean: 39.94 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 3 3 4845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.38
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it4.81
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44

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