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- PDB-3l1n: Crystal structure of Mp1p ligand binding domain 2 complexd with p... -

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Basic information

Entry
Database: PDB / ID: 3l1n
TitleCrystal structure of Mp1p ligand binding domain 2 complexd with palmitic acid
ComponentsCell wall antigen
KeywordsLIPID BINDING PROTEIN / helix-turn-helix / protein-ligand complex
Function / homology
Function and homology information


structural constituent of cell wall / yeast-form cell wall / hyphal cell wall / fungal-type cell wall organization / fungal-type cell wall / fatty acid binding / extracellular region
Similarity search - Function
Monooxygenase - #140 / Helix Hairpins - #790 / Cell wall mannoprotein 1 / Hydrophobic surface binding protein A / Monooxygenase / Helix Hairpins / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PALMITIC ACID / Cell wall mannoprotein 1
Similarity search - Component
Biological speciesPenicillium marneffei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsLiao, S. / Tung, E.T. / Zheng, W. / Chong, K. / Xu, Y. / Bartlam, M. / Rao, Z. / Yuen, K.Y.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of the Mp1p ligand binding domain 2 reveals its function as a fatty acid-binding protein.
Authors: Liao, S. / Tung, E.T. / Zheng, W. / Chong, K. / Xu, Y. / Dai, P. / Guo, Y. / Bartlam, M. / Yuen, K.Y. / Rao, Z.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4602
Polymers21,2041
Non-polymers2561
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cell wall antigen
hetero molecules

A: Cell wall antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9214
Polymers42,4082
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6550 Å2
ΔGint-44 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.510, 46.510, 149.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-399-

HOH

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Components

#1: Protein Cell wall antigen / Mp1p


Mass: 21204.037 Da / Num. of mol.: 1 / Fragment: ligand binding domain 2 / Mutation: I207M,L276M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium marneffei (fungus) / Strain: PM4 / Gene: MP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O42721
#2: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 1.9 Å3/Da / Density % sol: 35.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 11% polyethylene glycol(PEG)8000, 0.1M HEPES(pH 7.5), 8% ethylene glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97894 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 1.3→19.74 Å / Num. all: 41553 / Num. obs: 40950 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.2 % / Rmerge(I) obs: 0.079
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 5.5 / Num. unique all: 4048 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.3→19.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.376 / SU ML: 0.028 / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.052 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19755 1979 5 %RANDOM
Rwork0.18162 ---
all0.18456 40950 --
obs0.18242 37257 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 18 243 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221245
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9881683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7645167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09727.03754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63915240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.429154
X-RAY DIFFRACTIONr_chiral_restr0.0640.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02910
X-RAY DIFFRACTIONr_nbd_refined0.2080.2625
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.227
X-RAY DIFFRACTIONr_mcbond_it0.9191.5804
X-RAY DIFFRACTIONr_mcangle_it1.27821274
X-RAY DIFFRACTIONr_scbond_it2.1023464
X-RAY DIFFRACTIONr_scangle_it3.0094.5402
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 132 -
Rwork0.171 2357 -
obs--100 %

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