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- PDB-4yf5: Crystal structure of Rv1284 in the presence of polycarpine at aci... -

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Basic information

Entry
Database: PDB / ID: 4yf5
TitleCrystal structure of Rv1284 in the presence of polycarpine at acidic pH
ComponentsBeta-carbonic anhydrase 1
KeywordsLYASE / beta-carbonic anhydrase
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-carbonic anhydrase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHofmann, A.
CitationJournal: Febs J. / Year: 2015
Title: Chemical probing suggests redox-regulation of the carbonic anhydrase activity of mycobacterial Rv1284.
Authors: Nienaber, L. / Cave-Freeman, E. / Cross, M. / Mason, L. / Bailey, U.M. / Amani, P. / A Davis, R. / Taylor, P. / Hofmann, A.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-carbonic anhydrase 1
B: Beta-carbonic anhydrase 1
C: Beta-carbonic anhydrase 1
D: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2258
Polymers77,0234
Non-polymers2024
Water4,486249
1
A: Beta-carbonic anhydrase 1
B: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6134
Polymers38,5122
Non-polymers1012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-94 kcal/mol
Surface area13070 Å2
MethodPISA
2
C: Beta-carbonic anhydrase 1
D: Beta-carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6134
Polymers38,5122
Non-polymers1012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-94 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.289, 153.932, 159.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-322-

HOH

31C-303-

HOH

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Components

#1: Protein
Beta-carbonic anhydrase 1 / Beta-CA 1 / Carbonate dehydratase 1 / mtCA 1


Mass: 19255.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: mtcA1, canA, MT1322 / Plasmid: pCR T7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21AI / References: UniProt: P9WPJ6, carbonic anhydrase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% PEG 400, 0.1 M NaH2PO4/Na-citrate, 10 mM polycarpine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95375 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 2→24.6 Å / Num. obs: 81481 / % possible obs: 99.2 % / Redundancy: 13.7 % / Rsym value: 0.074 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.6 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLK

1ylk


Resolution: 2→24.561 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 4121 5.06 %
Rwork0.1973 --
obs0.2004 81481 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→24.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 4 249 5337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085186
X-RAY DIFFRACTIONf_angle_d1.1137040
X-RAY DIFFRACTIONf_dihedral_angle_d12.9421922
X-RAY DIFFRACTIONf_chiral_restr0.044816
X-RAY DIFFRACTIONf_plane_restr0.006919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02350.31291600.26752734X-RAY DIFFRACTION99
2.0235-2.04820.30881390.25032671X-RAY DIFFRACTION100
2.0482-2.07410.25021460.22882705X-RAY DIFFRACTION99
2.0741-2.10140.36641480.23262687X-RAY DIFFRACTION99
2.1014-2.13020.33691260.23562688X-RAY DIFFRACTION100
2.1302-2.16060.32751420.24952731X-RAY DIFFRACTION100
2.1606-2.19280.34061450.25212691X-RAY DIFFRACTION100
2.1928-2.22710.41731110.36942155X-RAY DIFFRACTION81
2.2271-2.26350.58081410.47812424X-RAY DIFFRACTION89
2.2635-2.30250.34481310.29792452X-RAY DIFFRACTION90
2.3025-2.34440.321740.21622617X-RAY DIFFRACTION100
2.3444-2.38940.28561530.20352733X-RAY DIFFRACTION100
2.3894-2.43820.23061370.18842719X-RAY DIFFRACTION100
2.4382-2.49110.34721420.20072690X-RAY DIFFRACTION100
2.4911-2.5490.31021600.20892690X-RAY DIFFRACTION100
2.549-2.61270.26851380.22162715X-RAY DIFFRACTION100
2.6127-2.68330.28681380.20512700X-RAY DIFFRACTION100
2.6833-2.76210.29321700.20242684X-RAY DIFFRACTION100
2.7621-2.85110.29371480.19932711X-RAY DIFFRACTION100
2.8511-2.95290.23381300.2022719X-RAY DIFFRACTION100
2.9529-3.07090.23621410.18052752X-RAY DIFFRACTION100
3.0709-3.21040.23821200.19252703X-RAY DIFFRACTION100
3.2104-3.37920.2531330.18132721X-RAY DIFFRACTION100
3.3792-3.59030.21651430.17182704X-RAY DIFFRACTION100
3.5903-3.86660.1991380.1662717X-RAY DIFFRACTION100
3.8666-4.25390.17581240.14542725X-RAY DIFFRACTION100
4.2539-4.86530.20251600.12642703X-RAY DIFFRACTION100
4.8653-6.11410.16911430.14862715X-RAY DIFFRACTION100
6.1141-24.56250.19231400.1612704X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2312-0.0307-0.01150.1962-0.04570.46090.13950.0773-0.0111-0.11230.08620.0287-0.04720.00020.30740.1196-0.0189-0.00430.0813-0.02380.1034-0.4294-36.2696-17.1685
20.21150.064-0.06550.2984-0.02180.5922-0.073-0.15-0.01380.1546-0.1930.0473-0.06010.1014-0.39590.0717-0.05480.04840.05180.03610.0923-28.57370.1824-22.8623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B
2X-RAY DIFFRACTION2chain C or chain D

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