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- PDB-2fwv: Crystal Structure of Rv0813 -

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Basic information

Entry
Database: PDB / ID: 2fwv
TitleCrystal Structure of Rv0813
Componentshypothetical protein MtubF_01000852
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical / restricted to actinomycetes / fatty acid binding protein like / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


peroxynitrite isomerase activity / Isomerases; Other isomerases / intracellular transport / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Nitrobindin, bacteria/plant / THAP4-like, heme-binding beta-barrel domain / Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / UPF0678 fatty acid-binding protein-like protein MT0834 / Peroxynitrite isomerase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD with data collected on Se-Met crystal at 0.97895 A. / SAD / Resolution: 1.7 Å
AuthorsShepard, W. / Haouz, A. / Grana, M. / Buschiazzo, A. / Betton, J.M. / Cole, S.T. / Alzari, P.M. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Bacteriol. / Year: 2007
Title: The Crystal Structure of Rv0813c from Mycobacterium tuberculosis Reveals a New Family of Fatty Acid-Binding Protein-Like Proteins in Bacteria
Authors: Shepard, W. / Haouz, A. / Grana, M. / Buschiazzo, A. / Betton, J.M. / Cole, S.T. / Alzari, P.M.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jun 26, 2013Group: Derived calculations
Revision 1.4Sep 20, 2017Group: Refinement description / Category: software / Item: _software.version
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: hypothetical protein MtubF_01000852
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3706
Polymers23,9251
Non-polymers4455
Water5,639313
1
A: hypothetical protein MtubF_01000852
hetero molecules

A: hypothetical protein MtubF_01000852
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,74012
Polymers47,8512
Non-polymers88910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area6340 Å2
ΔGint2 kcal/mol
Surface area17550 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: hypothetical protein MtubF_01000852
hetero molecules

A: hypothetical protein MtubF_01000852
hetero molecules

A: hypothetical protein MtubF_01000852
hetero molecules

A: hypothetical protein MtubF_01000852
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,47924
Polymers95,7014
Non-polymers1,77820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_755-x+2,-y,z1
crystal symmetry operation15_645y+1,x-1,-z1
Buried area17250 Å2
ΔGint3 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.836, 65.836, 239.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-663-

HOH

21A-699-

HOH

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Components

#1: Protein hypothetical protein MtubF_01000852 / rv0813c


Mass: 23925.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rv0813c / Plasmid: pDEST17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O53827, UniProt: P9WFG9*PLUS
#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7154.66
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981hanging drop7.5NH4(2)SO4, pH 7.5, hanging drop, temperature 298K
2982hanging drop7.5NaCl, pH 7.5, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.97895
SYNCHROTRONESRF ID2920.97895
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 26, 2003
ADSC QUANTUM 2102CCDNov 11, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SILICON 111SINGLE WAVELENGTHMx-ray1
2SILICON 111SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 12.8 / Number: 52245 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / D res high: 2.7 Å / D res low: 46.611 Å / Num. obs: 7723 / % possible obs: 99.9
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
8.5446.6129498.80.0320.0325.4
6.048.5447899.80.0320.0326.3
4.936.0459499.90.0330.0336.6
4.274.9369899.90.030.036.8
3.824.2777799.90.040.046.8
3.493.828381000.0490.0496.9
3.233.499291000.070.077
3.023.239711000.0940.0947
2.853.0210511000.1390.1396.9
2.72.8510931000.1970.1976.7
ReflectionResolution: 1.7→50.833 Å / Num. all: 29663 / Num. obs: 29663 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 19.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 5.2 / Num. unique all: 4255 / Rsym value: 0.316 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se31.9360.3020.050.0210.276
2Se40.1230.6990.1340.0490.315
Phasing dmFOM : 0.54 / FOM acentric: 0.55 / FOM centric: 0.49 / Reflection: 7688 / Reflection acentric: 6173 / Reflection centric: 1515
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-19.9840.780.850.68357205152
4.8-7.70.740.80.581067777290
3.9-4.80.760.780.6712951021274
3.4-3.90.660.680.5513001069231
2.9-3.40.430.450.3422651907358
2.7-2.90.170.180.1414041194210

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMAC5.2.0019refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD with data collected on Se-Met crystal at 0.97895 A.
Resolution: 1.7→43.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.783 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.094 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1503 5.1 %RANDOM
Rwork0.181 ---
all0.183 29635 --
obs0.183 29635 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 30 313 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211559
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9722107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.72221.97476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24915239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.691520
X-RAY DIFFRACTIONr_chiral_restr0.1230.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021202
X-RAY DIFFRACTIONr_nbd_refined0.2140.2705
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.247
X-RAY DIFFRACTIONr_mcbond_it1.1371.5961
X-RAY DIFFRACTIONr_mcangle_it1.81621497
X-RAY DIFFRACTIONr_scbond_it2.6033683
X-RAY DIFFRACTIONr_scangle_it3.9844.5610
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 102 -
Rwork0.231 2042 -
obs-2144 100 %

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