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- PDB-3hys: Structure of Rv0554 from Mycobacterium tuberculosis complexed wit... -

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Basic information

Entry
Database: PDB / ID: 3hys
TitleStructure of Rv0554 from Mycobacterium tuberculosis complexed with Malonic Acid
Componentsprotein Rv0554, putative Bromoperoxidase
KeywordsHYDROLASE / Oxidoreductase / Peroxidase
Function / homology
Function and homology information


bromide peroxidase activity
Similarity search - Function
Alpha/beta hydrolase family / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Putative non-heme bromoperoxidase BpoC / Putative non-heme bromoperoxidase BpoC
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsJohnston, J.M. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis.
Authors: Johnston, J.M. / Jiang, M. / Guo, Z. / Baker, E.N.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Feb 21, 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_struct_conn_angle / software / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _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: protein Rv0554, putative Bromoperoxidase
B: protein Rv0554, putative Bromoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,32014
Polymers64,5092
Non-polymers81112
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-34 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.435, 100.435, 135.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein protein Rv0554, putative Bromoperoxidase / POSSIBLE PEROXIDASE BPOC (NON-HAEM PEROXIDASE)


Mass: 32254.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: bpoC, MT0580, Rv0554 / Production host: Escherichia coli (E. coli)
References: UniProt: O06420, UniProt: P9WNH1*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 5 types, 400 molecules

#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.92
Details: 95% (0.1M NaAcetate pH 4.92, 2% MPD, 15% Ethylene glycol) and 5% Malonic acid 1.65M, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 31386 / % possible obs: 99.8 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.059 / Χ2: 0.978 / Net I/σ(I): 35.603
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 7.6 / Num. unique all: 3083 / Χ2: 0.935 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.43 Å48.94 Å
Translation2.43 Å48.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.155 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.868 / SU R Cruickshank DPI: 0.245 / SU Rfree: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1579 5 %RANDOM
Rwork0.166 ---
obs0.169 31347 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.41 Å2 / Biso mean: 27.222 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 52 388 4540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224255
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9635785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70523.179195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17715633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6781538
X-RAY DIFFRACTIONr_chiral_restr0.1390.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213322
X-RAY DIFFRACTIONr_mcbond_it1.121.52683
X-RAY DIFFRACTIONr_mcangle_it1.95124307
X-RAY DIFFRACTIONr_scbond_it3.37931572
X-RAY DIFFRACTIONr_scangle_it5.0524.51475
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 105 -
Rwork0.184 2158 -
all-2263 -
obs--100 %
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)
11.94540.8072-0.18460.7216-0.30310.37-0.05870.1241-0.2597-0.13150.0287-0.06130.1856-0.03510.03010.09190.00950.00170.0746-0.01310.0646-0.3771-48.1864-11.8476
20.8770.0865-0.20451.40150.29781.10040.0007-0.01210.0108-0.0080.00660.0629-0.0358-0.0703-0.00720.0357-0.01260.01280.04190.00160.0316-9.0478-41.5078-7.1605
30.85390.7522-0.9970.8854-1.08031.3474-0.02280.0605-0.0095-0.05970.01360.06110.0679-0.05630.00920.08740.0116-0.00770.0825-0.01340.0916-11.4835-34.2247-26.0976
41.1984-0.0763-0.37830.8367-0.18741.38070.0025-0.09010.01180.0901-0.0021-0.0344-0.030.0469-0.00050.0831-0.0057-0.00670.0559-0.00990.0854-2.7473-29.0427-6.3596
55.11250.38350.21946.0666-0.45750.2956-0.0213-0.40370.28460.5133-0.10660.21860.065-0.15360.12790.14160.0022-0.00220.15520.02370.1714.4443-46.98316.6995
60.72220.24290.1070.87320.02420.57780.0209-0.1471-0.05730.1745-0.015-0.00940.0527-0.0142-0.00580.09090.00710.00390.09910.00230.088726.5092-45.55664.4353
70.86260.0490.43560.82120.07582.34250.0070.0856-0.0582-0.092-0.03850.07240.0224-0.11380.03140.0916-0.01020.00460.09640.01290.124228.1724-26.8869-9.023
80.3122-0.0454-0.22610.86630.34730.35150.0008-0.02260.02130.03480.0095-0.1272-0.01470.0882-0.01030.0859-0.0060.00170.09780.00590.088935.2823-43.1363-1.0628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-13 - 43
2X-RAY DIFFRACTION2A44 - 127
3X-RAY DIFFRACTION3A128 - 187
4X-RAY DIFFRACTION4A188 - 261
5X-RAY DIFFRACTION5B2 - 8
6X-RAY DIFFRACTION6B9 - 122
7X-RAY DIFFRACTION7B123 - 169
8X-RAY DIFFRACTION8B170 - 262

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