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- PDB-5csd: Ligand binding domain 2 of Penicillium marneffei MP1 protein in c... -

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Basic information

Entry
Database: PDB / ID: 5csd
TitleLigand binding domain 2 of Penicillium marneffei MP1 protein in complex with arachidonic acids
ComponentsEnvelope glycoprotein
KeywordsLIPID BINDING PROTEIN / arachidonic acid / Ligand binding domain
Function / homologyCell wall mannoprotein 1 / Hydrophobic surface binding protein A / extracellular region / ARACHIDONIC ACID / Cell wall mannoprotein 1
Function and homology information
Biological speciesTalaromyces marneffei PM1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)69,71612
Polymers67,7054
Non-polymers2,0118
Water11,836657
1
A: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5353
Polymers16,9261
Non-polymers6092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5353
Polymers16,9261
Non-polymers6092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3233
Polymers16,9261
Non-polymers3972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3233
Polymers16,9261
Non-polymers3972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.502, 100.052, 99.050
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
11D-410-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA2 - 1591 - 158
21PROPROBB2 - 1591 - 158
12PROPROAA2 - 1591 - 158
22PROPROCC2 - 1591 - 158
13GLYGLYAA2 - 1581 - 157
23GLYGLYDD2 - 1581 - 157
14PROPROBB2 - 1591 - 158
24PROPROCC2 - 1591 - 158
15GLYGLYBB2 - 1581 - 157
25GLYGLYDD2 - 1581 - 157
16GLYGLYCC2 - 1581 - 157
26GLYGLYDD2 - 1581 - 157

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Envelope glycoprotein


Mass: 16926.221 Da / Num. of mol.: 4 / Fragment: UNP residues 187-345
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A093VKV7
#2: Chemical
ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H32O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 / 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: 1.45→50 Å / Num. obs: 100087 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Χ2: 1.076 / Net I/av σ(I): 15.889 / Net I/σ(I): 13.8 / Num. measured all: 393148
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.53.10.30395740.82795.8
1.5-1.563.80.25199900.88199.3
1.56-1.633.90.20499880.9699.6
1.63-1.723.90.159101011.06499.7
1.72-1.8340.127100441.12299.8
1.83-1.974.10.099100181.199.8
1.97-2.174.10.082101140.99499.9
2.17-2.484.20.079100711.147100
2.48-3.124.10.094101161.301100
3.12-5040.074100711.24498.5

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PHASER2.2.1phasing
PDB_EXTRACT3.15data extraction
Cootmodel building
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→44.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2173 / WRfactor Rwork: 0.1921 / FOM work R set: 0.8634 / SU B: 2.539 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0747 / SU Rfree: 0.0734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 4995 5 %RANDOM
Rwork0.1812 ---
obs0.1823 95019 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.51 Å2 / Biso mean: 18.396 Å2 / Biso min: 8.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20.02 Å2
2--0.14 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.45→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4741 0 144 657 5542
Biso mean--33.26 29.21 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195036
X-RAY DIFFRACTIONr_bond_other_d0.0120.025153
X-RAY DIFFRACTIONr_angle_refined_deg1.6732.0056793
X-RAY DIFFRACTIONr_angle_other_deg1.964311911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5035673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81327.033209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75415914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7421517
X-RAY DIFFRACTIONr_chiral_restr0.090.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025802
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021039
X-RAY DIFFRACTIONr_mcbond_it0.6391.0422572
X-RAY DIFFRACTIONr_mcbond_other0.6361.0422571
X-RAY DIFFRACTIONr_mcangle_it1.0311.5563219
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192000.07
12B192000.07
21A173100.16
22C173100.16
31A173240.16
32D173240.16
41B172500.16
42C172500.16
51B172840.16
52D172840.16
61C189280.07
62D189280.07
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 335 -
Rwork0.235 6516 -
all-6851 -
obs--91.82 %
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)
10.5225-0.0049-0.06321.44550.80250.45440.02810.00850.10.0739-0.07650.10820.0475-0.04250.04840.0551-0.00020.01340.0125-0.01970.058-26.321-16.12512.216
20.518-0.0140.03951.38950.78670.45160.0326-0.0094-0.1044-0.076-0.08580.1075-0.0499-0.04930.05320.0560.0028-0.02130.0142-0.01970.0579-26.316-27.01937.304
30.30250.3892-0.32231.6011-0.97810.63320.01810.0164-0.00210.0601-0.0362-0.0501-0.03390.0090.01810.0355-0.0134-0.01460.00940.01360.0564-3.463-36.93437.529
40.3198-0.37890.32031.6058-0.9680.62150.0237-0.0116-0.0013-0.0531-0.0385-0.04350.03190.0120.01480.03510.01250.00750.00850.01230.0534-3.554-6.12611.996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 11
2X-RAY DIFFRACTION1A12 - 59
3X-RAY DIFFRACTION1A60 - 118
4X-RAY DIFFRACTION1A119 - 139
5X-RAY DIFFRACTION1A140 - 159
6X-RAY DIFFRACTION2B2 - 11
7X-RAY DIFFRACTION2B12 - 59
8X-RAY DIFFRACTION2B60 - 120
9X-RAY DIFFRACTION2B121 - 137
10X-RAY DIFFRACTION2B138 - 159
11X-RAY DIFFRACTION3C2 - 8
12X-RAY DIFFRACTION3C9 - 25
13X-RAY DIFFRACTION3C26 - 57
14X-RAY DIFFRACTION3C58 - 75
15X-RAY DIFFRACTION3C76 - 112
16X-RAY DIFFRACTION3C113 - 135
17X-RAY DIFFRACTION3C136 - 159
18X-RAY DIFFRACTION4D2 - 8
19X-RAY DIFFRACTION4D9 - 25
20X-RAY DIFFRACTION4D26 - 58
21X-RAY DIFFRACTION4D59 - 75
22X-RAY DIFFRACTION4D76 - 112
23X-RAY DIFFRACTION4D113 - 136
24X-RAY DIFFRACTION4D137 - 160

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