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- PDB-5j5l: CRYSTAL STRUCTURE OF AFMP4P IN COMPLEX WITH ARACHIDONIC ACID -

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Basic information

Entry
Database: PDB / ID: 5j5l
TitleCRYSTAL STRUCTURE OF AFMP4P IN COMPLEX WITH ARACHIDONIC ACID
ComponentsUncharacterized protein
KeywordsLIPID BINDING PROTEIN / VIRULENCE FACTOR / ARACHIDONIC ACID
Function / homologyCell wall mannoprotein 1 / Hydrophobic surface binding protein A / extracellular region / ARACHIDONIC ACID / Cell wall mannoprotein 1
Function and homology information
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8682
Polymers16,5631
Non-polymers3041
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint2 kcal/mol
Surface area6830 Å2
Unit cell
Length a, b, c (Å)124.374, 124.374, 124.374
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-345-

HOH

21A-415-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 16563.178 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 44-194
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: PETH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4WZA5
#2: Chemical ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 298 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: 1.7→50 Å / Num. obs: 18323 / % possible obs: 99.7 % / Redundancy: 23 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 23 % / Rmerge(I) obs: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JOW

4jow
PDB Unreleased entry


Resolution: 1.7→44.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.387 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.19 938 5.1 %RANDOM
Rwork0.163 ---
obs0.165 18318 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 22 204 1308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021113
X-RAY DIFFRACTIONr_bond_other_d0.0010.021079
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.9821513
X-RAY DIFFRACTIONr_angle_other_deg0.7532492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9655153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1628.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64915179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02210
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_it1.3754.561609
X-RAY DIFFRACTIONr_mcbond_other1.2874.548608
X-RAY DIFFRACTIONr_mcangle_it1.6925.119760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 54 -
Rwork0.183 1273 -
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)
116.01411.576-2.737313.2526-0.96211.7429-0.0515-0.0165-0.26570.0081-0.0805-0.34230.09220.29260.1320.01230.0220.00940.09040.03440.024411.71682.83418.264
25.69454.81630.46576.48650.29932.7780.1216-0.3181-0.28550.2845-0.2137-0.18770.30450.22330.09210.05470.02580.01790.04230.0290.02992.24675.98924.157
316.18898.93526.006311.25712.50776.79390.1484-0.18431.48860.3901-0.57480.4031-0.01440.47470.42640.0434-0.02630.02340.09310.0050.222615.33196.19915.025
411.62359.2763-3.920112.7811-6.34227.2036-0.19320.65570.3537-0.1430.42170.35590.1055-0.112-0.22850.0229-0.007-0.00910.04010.01730.0132-6.37578.415.571
56.06121.5623-0.20632.4097-0.79811.1022-0.0977-0.15930.8984-0.01250.09810.2077-0.1224-0.0633-0.00040.0517-0.0088-0.00410.021-0.0320.1398-1.77990.2821.374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 44
2X-RAY DIFFRACTION2A45 - 81
3X-RAY DIFFRACTION3A82 - 97
4X-RAY DIFFRACTION4A98 - 121
5X-RAY DIFFRACTION5A122 - 176

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