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- PDB-4xfw: Crystal structure of the monoclinic form of alpha-carbonic anhydr... -

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Basic information

Entry
Database: PDB / ID: 4xfw
TitleCrystal structure of the monoclinic form of alpha-carbonic anhydrase from the human pathogen Helicobacter pylori
ComponentsAlpha-carbonic anhydrase
KeywordsLYASE / Helicobacter pylori / carbonic anhydrase / metallo proteins
Function / homology
Function and homology information


carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / 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
ACETIC ACID / Alpha-carbonic anhydrase
Similarity search - Component
Biological speciesHelicobacter pylori G27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.517 Å
AuthorsCompostella, M.E. / Vallese, F. / Berto, P. / Zanotti, G.
Funding support Italy, 2items
OrganizationGrant numberCountry
MIURUnraveling structural and functional determinants behind Helicobacter pylori pathogenesis and persistence Italy
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of alpha-carbonic anhydrase from the human pathogen Helicobacter pylori.
Authors: Compostella, M.E. / Berto, P. / Vallese, F. / Zanotti, G.
History
DepositionDec 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-carbonic anhydrase
B: Alpha-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7818
Polymers52,4242
Non-polymers3586
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-125 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.906, 95.905, 53.318
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-carbonic anhydrase


Mass: 26211.781 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Gene: HPG27_1129 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5Z8I0

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Non-polymers , 5 types, 668 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium Nitrate, 0.1 M Bis Tris propane pH 8.5 and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.517→47.96 Å / Num. all: 67218 / Num. obs: 67218 / % possible obs: 96.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 18.5
Reflection shellResolution: 1.517→1.62 Å / Redundancy: 3 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G7A

4g7a


Resolution: 1.517→47.953 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 3384 5.04 %Random selection
Rwork0.1696 ---
obs0.1711 67175 96.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.517→47.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 13 662 4382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073842
X-RAY DIFFRACTIONf_angle_d1.1525199
X-RAY DIFFRACTIONf_dihedral_angle_d14.2011439
X-RAY DIFFRACTIONf_chiral_restr0.049537
X-RAY DIFFRACTIONf_plane_restr0.006679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5171-1.53870.3212810.26311551X-RAY DIFFRACTION56
1.5387-1.56170.27881590.24282652X-RAY DIFFRACTION97
1.5617-1.58610.28211400.22892680X-RAY DIFFRACTION97
1.5861-1.61210.28111350.21782710X-RAY DIFFRACTION98
1.6121-1.63990.22981380.21162618X-RAY DIFFRACTION97
1.6399-1.66970.25321450.21592726X-RAY DIFFRACTION98
1.6697-1.70190.27881510.20952651X-RAY DIFFRACTION98
1.7019-1.73660.22711520.20572683X-RAY DIFFRACTION98
1.7366-1.77440.22311410.18792720X-RAY DIFFRACTION98
1.7744-1.81560.22351430.19382667X-RAY DIFFRACTION98
1.8156-1.8610.2361300.19452727X-RAY DIFFRACTION98
1.861-1.91140.21511270.1842691X-RAY DIFFRACTION98
1.9114-1.96760.21451150.18192749X-RAY DIFFRACTION98
1.9676-2.03110.2111470.17342713X-RAY DIFFRACTION98
2.0311-2.10370.21241480.17912678X-RAY DIFFRACTION99
2.1037-2.18790.20071430.16852731X-RAY DIFFRACTION99
2.1879-2.28750.20911510.17262688X-RAY DIFFRACTION99
2.2875-2.40810.18581570.16762717X-RAY DIFFRACTION99
2.4081-2.5590.18261410.17162728X-RAY DIFFRACTION99
2.559-2.75650.21341600.17142701X-RAY DIFFRACTION98
2.7565-3.03390.18021420.16852731X-RAY DIFFRACTION99
3.0339-3.47280.18691620.15472720X-RAY DIFFRACTION99
3.4728-4.37490.17661450.13762763X-RAY DIFFRACTION99
4.3749-47.97640.14691310.14612796X-RAY DIFFRACTION99

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