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- PDB-5fb7: Ligand binding domain 2 of Penicillium marneffei MP1 protein comp... -

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Basic information

Entry
Database: PDB / ID: 5fb7
TitleLigand binding domain 2 of Penicillium marneffei MP1 protein complexed with multiple arachidonic acids
ComponentsEnvelope glycoprotein
KeywordsLIPID BINDING PROTEIN / Ligand binding domain 2 / multiple arachidonic acids
Function / homologyCell wall mannoprotein 1 / Hydrophobic surface binding protein A / ARACHIDONIC ACID / Envelope glycoprotein
Function and homology information
Biological speciesTalaromyces marneffei PM1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLam, W.H. / Zhang, H. / Hao, Q.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Talaromyces marneffei Mp1p Is a Virulence Factor that Binds and Sequesters a Key Proinflammatory Lipid to Dampen Host Innate Immune Response
Authors: Sze, K.H. / Lam, W.H. / Zhang, H. / Ke, Y.H. / Tse, M.K. / Woo, P.C. / Lau, S.K. / Lau, C.C. / Cai, J.P. / Tung, E.T. / Lo, R.K. / Xu, S. / Kao, R.Y. / Hao, Q. / Yuen, K.Y.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
C: Envelope glycoprotein
D: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,83512
Polymers66,3994
Non-polymers2,4368
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint16 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.239, 98.495, 100.120
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-360-

HOH

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Components

#1: Protein
Envelope glycoprotein


Mass: 16599.871 Da / Num. of mol.: 4 / Fragment: UNP residues 188-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces marneffei PM1 (fungus) / Gene: GQ26_0022220 / Plasmid: His-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A093VKV7
#2: Chemical
ChemComp-ACD / ARACHIDONIC ACID / Arachidonic acid


Mass: 304.467 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER KFX52825 IS FOR THIS SEQUENCE.

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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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 4000, sodium acetate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 90586 / % possible obs: 98.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.066 / Χ2: 1.088 / Net I/av σ(I): 26.115 / Net I/σ(I): 13 / Num. measured all: 668581
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.557.10.56791610.858100
1.55-1.627.40.44890770.881100
1.62-1.697.40.30691800.955100
1.69-1.787.50.2190771.028100
1.78-1.897.50.13891341.131100
1.89-2.047.50.09191801.164100
2.04-2.247.50.06391191.304100
2.24-2.567.60.06691501.333100
2.56-3.237.40.07491301.03399.4
3.23-506.90.04583781.18690.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CSD

5csd


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2358 / WRfactor Rwork: 0.2039 / FOM work R set: 0.831 / SU B: 3.626 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0839 / SU Rfree: 0.0826 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 4549 5 %RANDOM
Rwork0.191 ---
obs0.1923 86037 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 77.07 Å2 / Biso mean: 30.275 Å2 / Biso min: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-0.16 Å2
2---1.55 Å2-0 Å2
3---1.8 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 176 427 5195
Biso mean--40.25 36.08 -
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194952
X-RAY DIFFRACTIONr_bond_other_d0.0080.025112
X-RAY DIFFRACTIONr_angle_refined_deg1.4322.0116674
X-RAY DIFFRACTIONr_angle_other_deg1.162311809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2465660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76627.115208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4915902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0581516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025712
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021036
X-RAY DIFFRACTIONr_mcbond_it1.2241.2662496
X-RAY DIFFRACTIONr_mcbond_other1.2191.2652495
X-RAY DIFFRACTIONr_mcangle_it1.771.8923126
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 326 -
Rwork0.254 6390 -
all-6716 -
obs--98.85 %
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)
11.5661-0.04360.66911.59770.67561.19440.1652-0.0187-0.19060.06910.07790.21630.1021-0.0192-0.24310.11580.00320.02160.16570.02720.167-25.89317.019-12.464
21.45930.097-0.62951.36430.56581.17460.15350.01310.1586-0.0610.06710.1964-0.0898-0.0147-0.22060.1133-0.0019-0.01340.16130.02240.1336-25.91726.846-37.648
30.53060.7674-0.48623.8294-1.87331.20230.0536-0.00410.16960.02750.00830.3321-0.0782-0.0078-0.06190.0871-0.00760.01140.11710.02090.1378-3.0576.192-12.466
40.4154-0.75640.45083.7618-1.79631.18720.05110.0057-0.1656-0.03080.00610.33490.0823-0.0105-0.05720.0840.00710.00290.11460.02260.1361-3.04737.542-37.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 52
2X-RAY DIFFRACTION1A53 - 64
3X-RAY DIFFRACTION1A65 - 107
4X-RAY DIFFRACTION1A108 - 136
5X-RAY DIFFRACTION1A137 - 157
6X-RAY DIFFRACTION2B7 - 52
7X-RAY DIFFRACTION2B53 - 90
8X-RAY DIFFRACTION2B91 - 106
9X-RAY DIFFRACTION2B107 - 136
10X-RAY DIFFRACTION2B137 - 157
11X-RAY DIFFRACTION3C6 - 38
12X-RAY DIFFRACTION3C39 - 56
13X-RAY DIFFRACTION3C57 - 79
14X-RAY DIFFRACTION3C80 - 104
15X-RAY DIFFRACTION3C105 - 147
16X-RAY DIFFRACTION3C148 - 157
17X-RAY DIFFRACTION4D6 - 38
18X-RAY DIFFRACTION4D39 - 72
19X-RAY DIFFRACTION4D73 - 97
20X-RAY DIFFRACTION4D98 - 136
21X-RAY DIFFRACTION4D137 - 157

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