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- PDB-5e7x: Ligand binding domain 1 of Penicillium marneffei MP1 protein in c... -

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Basic information

Entry
Database: PDB / ID: 5e7x
TitleLigand binding domain 1 of Penicillium marneffei MP1 protein in complex with palmitic acid
ComponentsCell wall antigen
KeywordsLIPID BINDING PROTEIN / palmitic acid / MP1
Function / homologyCell wall mannoprotein 1 / Hydrophobic surface binding protein A / extracellular region / ACETATE ION / PALMITIC ACID / Envelope glycoprotein / Cell wall antigen
Function and homology information
Biological speciesTalaromyces marneffei PM1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLam, W.H. / Zhang, H. / Hao, Q.
CitationJournal: Infect. Immun. / Year: 2019
Title: Talaromyces marneffeiMp1 protein, a novel virulence factor, carries two arachidonic acid-binding domains to suppress inflammatory responses in hosts.
Authors: Lam, W.H. / Sze, K.H. / Ke, Y. / Tse, M.K. / Zhang, H. / Woo, P.C.Y. / Lau, S.K.P. / Lau, C.C.Y. / Xu, S. / Lai, P.M. / Zhou, T. / Antonyuk, S.V. / Kao, R.Y.T. / Yuen, K.Y. / Hao, Q.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 2.0Mar 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / diffrn_source / entity / entity_src_gen / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_oper_list / struct_conf / struct_ref / struct_ref_seq / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_fragment / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_site_gen.auth_seq_id
Revision 2.1Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Cell wall antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7754
Polymers16,3681
Non-polymers4083
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-1 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.580, 52.580, 57.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cell wall antigen


Mass: 16367.681 Da / Num. of mol.: 1 / Fragment: UNP residues 27-181
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, UniProt: A8HBN5*PLUS
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 12000, sodium acetate, ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→38.86 Å / Num. obs: 14575 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.066 Å2 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.019 / Net I/σ(I): 22.8 / Num. measured all: 53561
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.8-1.853.80.5182.2416210990.3499.9
8.05-38.863.60.01173.46241740.00797.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2171 / WRfactor Rwork: 0.1769 / FOM work R set: 0.8425 / SU B: 5.933 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1235 / SU Rfree: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 733 5 %RANDOM
Rwork0.1792 ---
obs0.1813 13818 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.4 Å2 / Biso mean: 36.532 Å2 / Biso min: 22.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0 Å2
2--0.58 Å2-0 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.8→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 28 66 1245
Biso mean--48.43 41.49 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191193
X-RAY DIFFRACTIONr_bond_other_d0.0010.021218
X-RAY DIFFRACTIONr_angle_refined_deg1.15321610
X-RAY DIFFRACTIONr_angle_other_deg0.74332818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4665154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35827.55645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04715207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091151
X-RAY DIFFRACTIONr_chiral_restr0.0570.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_mcbond_it1.482.986620
X-RAY DIFFRACTIONr_mcbond_other1.4812.974618
X-RAY DIFFRACTIONr_mcangle_it2.2714.45772
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 63 -
Rwork0.254 1035 -
all-1098 -
obs--99.73 %
Refinement TLS params.Method: refined / Origin x: -44.3449 Å / Origin y: 80.2174 Å / Origin z: 4.2136 Å
111213212223313233
T0.0372 Å20.0207 Å2-0.0128 Å2-0.032 Å2-0.0296 Å2--0.0294 Å2
L0.6349 °2-0.4402 °20.2615 °2-0.4754 °2-0.3375 °2--0.4314 °2
S-0.0567 Å °-0.0514 Å °0.0315 Å °-0.0357 Å °-0.0019 Å °0.0003 Å °0.0443 Å °-0.0478 Å °0.0586 Å °

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