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- PDB-1r88: The crystal structure of Mycobacterium tuberculosis MPT51 (FbpC1) -

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Basic information

Entry
Database: PDB / ID: 1r88
TitleThe crystal structure of Mycobacterium tuberculosis MPT51 (FbpC1)
ComponentsMPT51/MPB51 antigen
KeywordsIMMUNE SYSTEM / Mycobacterium tuberculosis / alfa/beta hydrolase fold / antigen 85 / MPT51 / FBPC1
Function / homology
Function and homology information


mycolate cell wall layer assembly / zymogen binding / acyltransferase activity, transferring groups other than amino-acyl groups / fibronectin binding / extracellular region
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MPT51/MPB51 antigen / MPT51/MPB51 antigen
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsWilson, R.A. / Maughan, W.N. / Kremer, L. / Besra, G.S. / Futterer, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The structure of Mycobacterium tuberculosis MPT51 (FbpC1) defines a new family of non-catalytic alpha/beta hydrolases.
Authors: Wilson, R.A. / Maughan, W.N. / Kremer, L. / Besra, G.S. / Futterer, K.
History
DepositionOct 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPT51/MPB51 antigen
B: MPT51/MPB51 antigen


Theoretical massNumber of molelcules
Total (without water)58,9132
Polymers58,9132
Non-polymers00
Water7,206400
1
A: MPT51/MPB51 antigen


Theoretical massNumber of molelcules
Total (without water)29,4571
Polymers29,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MPT51/MPB51 antigen


Theoretical massNumber of molelcules
Total (without water)29,4571
Polymers29,4571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.900, 108.900, 109.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 33 - 281 / Label seq-ID: 8 - 256

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a monomer, represented by either of the two molecules in the asymmetric unit

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Components

#1: Protein MPT51/MPB51 antigen / fibronectin-binding protein C1 (FbpC1 / MPT51)


Mass: 29456.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fbpC1 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P0A4V6, UniProt: P9WQN7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18-10 %(w/v)PEG80001reservoir
28-10 %(v/v)MPD1reservoir
32.5 %(v/v)isopropanol1reservoir
4200 mMsodium acetate1reservoirpH4.6
5100 mMsodium citrate1reservoirpH5.0
670 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 78268 / Num. obs: 78268 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.489 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 493963 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.489

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1dqz

1dqz


Resolution: 1.71→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.164 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20533 3668 5 %RANDOM
Rwork0.1887 ---
obs0.18954 69287 93.3 %-
all-69287 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.208 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20 Å2
2---1.31 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.71→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 0 400 4336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214070
X-RAY DIFFRACTIONr_bond_other_d0.0020.023424
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.8995562
X-RAY DIFFRACTIONr_angle_other_deg0.75337938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475532
X-RAY DIFFRACTIONr_chiral_restr0.060.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024798
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02882
X-RAY DIFFRACTIONr_nbd_refined0.1820.2851
X-RAY DIFFRACTIONr_nbd_other0.2220.24006
X-RAY DIFFRACTIONr_nbtor_other0.080.22008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.231
X-RAY DIFFRACTIONr_mcbond_it0.1731.52626
X-RAY DIFFRACTIONr_mcangle_it0.32924116
X-RAY DIFFRACTIONr_scbond_it0.6131444
X-RAY DIFFRACTIONr_scangle_it0.9194.51446
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3430 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.065
loose thermal0.2110
LS refinement shellResolution: 1.706→1.798 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.254 472
Rwork0.243 8757
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)
10.8557-0.3689-0.27511.63570.09590.8622-0.0359-0.0233-0.06550.0120.01710.00110.08730.03160.01880.00230.0106-0.00240.0485-0.00560.057427.488932.244829.0048
20.75310.19580.33160.86260.09161.6703-0.03350.07760.006-0.09580.03040.02060.008-0.0160.00320.0109-0.0083-0.00740.051-0.01040.06347.09942.145460.0301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 2818 - 256
2X-RAY DIFFRACTION2BB33 - 2818 - 256
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.96
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å

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