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- PDB-5zxa: Crystal structure of fibronectin-binding protein Apa mutant from ... -

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Basic information

Entry
Database: PDB / ID: 5zxa
TitleCrystal structure of fibronectin-binding protein Apa mutant from Mycobacterium tuberculosis
ComponentsAlanine and proline-rich secreted protein Apa
KeywordsPROTEIN BINDING / substrate binding / Cyclolavandulyl diphosphate synthase / inhibitor
Function / homologyFibronectin-attachment / Fibronectin-attachment protein (FAP) domain / extracellular matrix binding / cellular response to starvation / cell surface / extracellular region / : / Alanine and proline-rich secreted protein Apa
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsGao, J. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Functional and structural investigations of fibronectin-binding protein Apa from Mycobacterium tuberculosis.
Authors: Kuo, C.J. / Gao, J. / Huang, J.W. / Ko, T.P. / Zhai, C. / Ma, L. / Liu, W. / Dai, L. / Chang, Y.F. / Chen, T.H. / Hu, Y. / Yu, X. / Guo, R.T. / Chen, C.C.
History
DepositionMay 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine and proline-rich secreted protein Apa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0663
Polymers32,7741
Non-polymers2932
Water3,117173
1
A: Alanine and proline-rich secreted protein Apa
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)198,39818
Polymers196,6416
Non-polymers1,75612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area13880 Å2
ΔGint-194 kcal/mol
Surface area38860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.028, 118.028, 118.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

21A-664-

HOH

31A-672-

HOH

41A-673-

HOH

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Components

#1: Protein Alanine and proline-rich secreted protein Apa / 45 kDa glycoprotein / 45/47 kDa antigen / Antigen MPT-32 / FAP-B / Fibronectin attachment protein / ...45 kDa glycoprotein / 45/47 kDa antigen / Antigen MPT-32 / FAP-B / Fibronectin attachment protein / Immunogenic protein MPT32


Mass: 32773.582 Da / Num. of mol.: 1 / Mutation: A160C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: 1860c / Plasmid: pET46Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WIR7
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#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.: 173 / 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: 2.43 Å3/Da / Density % sol: 49.44 % / Mosaicity: 0.31 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M NaCit, 2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 29, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→25 Å / Num. obs: 31151 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Χ2: 0.819 / Net I/σ(I): 11.4 / Num. measured all: 191611
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.835.90.4231010.9030.1830.4590.40199.9
1.83-1.916.20.30630700.9660.1290.3330.434100
1.91-1.996.20.1930920.9850.080.2070.472100
1.99-2.16.20.13230970.9920.0560.1430.533100
2.1-2.236.20.0931050.9960.0380.0980.648100
2.23-2.46.20.07131010.9970.0310.0780.775100
2.4-2.646.20.05930960.9970.0260.0650.947100
2.64-3.036.20.05531260.9970.0240.060.897100
3.03-3.816.10.05931520.9960.0270.0651.338100
3.81-2560.04532110.9980.020.0491.72999.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data scaling
CNSphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.77→23.665 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.19 / Stereochemistry target values: ML
Details: The SF file contains fridiel pairs under I_plus/minus columns.
RfactorNum. reflection% reflection
Rfree0.181 3007 5 %
Rwork0.1632 57176 -
obs0.1641 60183 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.25 Å2 / Biso mean: 32.9971 Å2 / Biso min: 14.65 Å2
Refinement stepCycle: final / Resolution: 1.77→23.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 7 173 1400
Biso mean--50.19 45.7 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181259
X-RAY DIFFRACTIONf_angle_d1.5011714
X-RAY DIFFRACTIONf_chiral_restr0.113182
X-RAY DIFFRACTIONf_plane_restr0.01225
X-RAY DIFFRACTIONf_dihedral_angle_d14.626739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7687-1.79770.26651430.25642729287299
1.7977-1.82870.21691430.226527132856100
1.8287-1.86190.19811470.19627152862100
1.8619-1.89770.20091420.181927232865100
1.8977-1.93640.18141430.16327462889100
1.9364-1.97850.17941390.15527072846100
1.9785-2.02450.16491460.153327562902100
2.0245-2.07510.18651430.15727382881100
2.0751-2.13120.18631440.156827222866100
2.1312-2.19390.18661410.149326972838100
2.1939-2.26460.15631460.148827302876100
2.2646-2.34550.17041420.159326922834100
2.3455-2.43930.16941440.165227612905100
2.4393-2.55020.22171470.1727412888100
2.5502-2.68450.20451410.165427052846100
2.6845-2.85240.20231430.168827202863100
2.8524-3.07220.1691470.177127242871100
3.0722-3.38060.18441440.15427372881100
3.3806-3.86790.16361410.150327242865100
3.8679-4.86620.14881420.14452701284399
4.8662-23.66660.20281390.18052695283498
Refinement TLS params.Method: refined / Origin x: 19.2733 Å / Origin y: 6.1454 Å / Origin z: 72.5014 Å
111213212223313233
T0.1573 Å2-0.0369 Å20.0055 Å2-0.164 Å2-0.0171 Å2--0.1658 Å2
L1.8939 °20.5106 °2-0.2116 °2-0.3503 °20.1608 °2--1.0909 °2
S0.1175 Å °-0.0934 Å °0.0473 Å °0.0435 Å °-0.0404 Å °-0.0469 Å °-0.0482 Å °0.0761 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA110 - 402
2X-RAY DIFFRACTION1allA501 - 673

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