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- PDB-5zx9: Crystal structure of apo form fibronectin-binding protein Apa fro... -

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Basic information

Entry
Database: PDB / ID: 5zx9
TitleCrystal structure of apo form fibronectin-binding protein Apa 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: 1.55 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)32,8342
Polymers32,7421
Non-polymers921
Water4,756264
1
A: Alanine and proline-rich secreted protein Apa
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)197,00212
Polymers196,4496
Non-polymers5536
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 area13850 Å2
ΔGint-88 kcal/mol
Surface area39750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.666, 118.666, 117.894
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-643-

HOH

21A-729-

HOH

31A-730-

HOH

41A-740-

HOH

51A-743-

HOH

61A-747-

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: 32741.518 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.44 Å3/Da / Density % sol: 49.58 % / Mosaicity: 0.865 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000, 0.1M HEPES pH 7.5, 0.2M (NH4)2SO4, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 46832 / % possible obs: 99.9 % / Redundancy: 16.8 % / Biso Wilson estimate: 25.51 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.016 / Rrim(I) all: 0.064 / Χ2: 1.078 / Net I/σ(I): 17.8 / Num. measured all: 787523
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.55-1.6113.40.99946450.8240.2811.152100
1.61-1.6716.20.72446470.9280.1851.171000.747
1.67-1.7516.40.546590.9630.1271.2161000.516
1.75-1.8416.70.30946690.9830.0781.0751000.319
1.84-1.95170.20446420.9920.0511.0251000.21
1.95-2.117.30.14946730.9950.0371.0821000.154
2.1-2.3117.70.10646800.9970.0261.0661000.11
2.31-2.6517.80.0847110.9980.0191.0821000.083
2.65-3.34180.07247070.9990.0170.9381000.074
3.342-2517.50.04147990.9990.011.0299.10.042

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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: 1.55→23.479 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1704 2000 4.27 %
Rwork0.1566 44822 -
obs0.1572 46822 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.26 Å2 / Biso mean: 35.0786 Å2 / Biso min: 18.29 Å2
Refinement stepCycle: final / Resolution: 1.55→23.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 6 264 1514
Biso mean--44.89 49.43 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161392
X-RAY DIFFRACTIONf_angle_d1.4571910
X-RAY DIFFRACTIONf_chiral_restr0.109204
X-RAY DIFFRACTIONf_plane_restr0.01253
X-RAY DIFFRACTIONf_dihedral_angle_d14.514844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5425-1.5810.27651400.22143149328998
1.581-1.62380.19691410.206131603301100
1.6238-1.67150.21161420.184631863328100
1.6715-1.72550.19361430.173631793322100
1.7255-1.78710.18771410.158231843325100
1.7871-1.85860.17381430.16331873330100
1.8586-1.94320.15771420.158531883330100
1.9432-2.04560.19511430.160332023345100
2.0456-2.17370.18351420.156732033345100
2.1737-2.34140.17321440.157331943338100
2.3414-2.57670.14961430.160132263369100
2.5767-2.9490.18611440.165532263370100
2.949-3.7130.17911450.149532433388100
3.713-23.4820.14711470.1473295344299
Refinement TLS params.Method: refined / Origin x: 19.1762 Å / Origin y: 5.8597 Å / Origin z: 72.1697 Å
111213212223313233
T0.1747 Å2-0.0311 Å2-0.0047 Å2-0.1851 Å2-0.0045 Å2--0.177 Å2
L1.4191 °20.2993 °20.0259 °2-0.6193 °20.1569 °2--0.9458 °2
S0.0652 Å °-0.0692 Å °0.0026 Å °0.0761 Å °-0.0181 Å °-0.0385 Å °-0.0311 Å °0.0718 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA110 - 401
2X-RAY DIFFRACTION1allA501 - 764

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