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- PDB-5j5k: CRYSTAL STRUCTURE OF AFMP4P IN COMPLEX WITH PALMITIC ACID -

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Basic information

Entry
Database: PDB / ID: 5j5k
TitleCRYSTAL STRUCTURE OF AFMP4P IN COMPLEX WITH PALMITIC ACID
ComponentsUncharacterized protein
KeywordsLIPID BINDING PROTEIN / VIRULENCE FACTOR / AFMP4 / PALMITIC ACID
Function / homologyCell wall mannoprotein 1 / Hydrophobic surface binding protein A / extracellular region / alpha-D-mannopyranose / PALMITIC ACID / Cell wall mannoprotein 1
Function and homology information
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, H. / Hao, Q.
CitationJournal: To Be Published
Title: A Novel Class Of Virulence Factors In Penicillium Marneffei And Aspergillus Fumigatus Enhances Intracellular Survival In Monocytes By Arachidonic Acid Binding
Authors: Zhang, H. / Hao, Q. / Lam, W.H.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3523
Polymers16,9161
Non-polymers4372
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint4 kcal/mol
Surface area6840 Å2
Unit cell
Length a, b, c (Å)124.836, 124.836, 124.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 16915.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 38-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_2G17630 / Plasmid: PPIC9K / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: Q4WZA5
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES PH 6.5, 25% POLYETHYLENE GLYCOL 4000, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 12425 / % possible obs: 99.8 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 19.9 % / Rmerge(I) obs: 0.433 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0110refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L1N

3l1n


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.354 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.184 601 4.8 %RANDOM
Rwork0.149 ---
obs0.151 12420 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 31.42 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 29 148 1254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221118
X-RAY DIFFRACTIONr_bond_other_d0.0010.02681
X-RAY DIFFRACTIONr_angle_refined_deg0.9681.9911522
X-RAY DIFFRACTIONr_angle_other_deg0.87131714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8155152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07428.7841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.03215179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5725753
X-RAY DIFFRACTIONr_mcbond_other0.8225306
X-RAY DIFFRACTIONr_mcangle_it2.2451206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7610365
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.65910315
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 53 -
Rwork0.185 852 -
obs--100 %
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)
114.03226.9764-2.147312.4215-0.04376.0530.0891-0.07770.00990.0769-0.1592-0.50910.09790.61770.07010.07890.02120.03940.18440.07570.073714.45685.27418.165
24.03083.1375-1.3626.229-2.21043.0807-0.0031-0.2174-0.1905-0.0046-0.2192-0.27870.29290.21520.22220.07280.03840.03740.10730.02940.06275.72680.51121.449
35.57422.2513-1.85225.9315-2.2815.1074-0.16630.46240.0613-0.43210.30840.22950.3589-0.402-0.14210.1208-0.0428-0.03720.0862-0.00340.0341-6.47278.38318.229
44.18211.4413-0.80842.9247-1.04941.970.0682-0.11360.56420.13360.02350.2699-0.2429-0.0289-0.09170.1449-0.0365-0.00940.0849-0.0260.087-0.18192.09420.625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 39
2X-RAY DIFFRACTION2A40 - 96
3X-RAY DIFFRACTION3A97 - 128
4X-RAY DIFFRACTION4A129 - 176

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