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- PDB-4coq: The complex of alpha-Carbonic anhydrase from Thermovibrio ammonif... -

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Basic information

Entry
Database: PDB / ID: 4coq
TitleThe complex of alpha-Carbonic anhydrase from Thermovibrio ammonificans with inhibitor sulfanilamide.
ComponentsCARBONATE DEHYDRATASE
KeywordsLYASE
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
Chem-PG6 / TRIETHYLENE GLYCOL / SULFANILAMIDE / Carbonic anhydrase
Similarity search - Component
Biological speciesTHERMOVIBRIO AMMONIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJames, P. / Isupov, M.N. / Sayer, C. / Berg, S. / Lioliou, M. / Kotlar, H. / Littlechild, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Structure of a Tetrameric [Alpha]-Carbonic Anhydrase from Thermovibrio Ammonificans Reveals a Core Formed Around Intermolecular Disulfides that Contribute to its Thermostability
Authors: James, P. / Isupov, M.N. / Sayer, C. / Saneei, V. / Berg, S. / Lioliou, M. / Kotlar, H. / Littlechild, J.
History
DepositionJan 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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_initial_refinement_model / 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_database_status.status_code_sf / _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_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 / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONATE DEHYDRATASE
B: CARBONATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,52214
Polymers55,4522
Non-polymers2,07112
Water12,412689
1
A: CARBONATE DEHYDRATASE
B: CARBONATE DEHYDRATASE
hetero molecules

A: CARBONATE DEHYDRATASE
B: CARBONATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,04528
Polymers110,9044
Non-polymers4,14124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10270 Å2
ΔGint-163.5 kcal/mol
Surface area40660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.050, 115.360, 65.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2046-

HOH

21B-2090-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.914, -0.407, 0.007), (-0.406, -0.913, -0.029), (0.018, 0.024, -1)
Vector: 22.80585, 111.11547, 25.40675)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CARBONATE DEHYDRATASE / ALPHA-CARBONIC ANHYDRASE


Mass: 27725.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOVIBRIO AMMONIFICANS (bacteria) / Strain: HB-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E8T502, carbonic anhydrase

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Non-polymers , 7 types, 701 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAN / SULFANILAMIDE


Mass: 172.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2O2S / Comment: antibiotic*YM
#4: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O6
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsSULFANILAMIDE (SAN): MODELLED WITH OCCUPANCY 0.35 DUE TO DISORDER

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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: 3.05 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growpH: 5.5
Details: 50 MM BIS-TRIS PROPANE, 100 MM NACL, 12.5% PEG3350 PH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→57.68 Å / Num. obs: 86560 / % possible obs: 94.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 67.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BALBESphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KOP

1kop


Resolution: 1.55→34.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.481 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20506 4317 5 %RANDOM
Rwork0.17574 ---
obs0.17723 81876 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.397 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--1.19 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 130 689 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194365
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9845954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50723.738206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02515808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.41529
X-RAY DIFFRACTIONr_chiral_restr0.0980.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.024.3711965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6917.3792493
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3665.5062399
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.555→1.595 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 222 -
Rwork0.265 4397 -
obs--69.28 %

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