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- PDB-5v50: Crystal Structure of MpPR-1i -

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Basic information

Entry
Database: PDB / ID: 5v50
TitleCrystal Structure of MpPR-1i
ComponentsPR-1 protein
KeywordsLIPID BINDING PROTEIN / pathogenesis-related protein 1 / Cacao infection
Function / homologySCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / PR-1 protein
Function and homology information
Biological speciesMoniliophthora perniciosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsLuo, Z. / Asojo, O.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)SMOLBnet 2.0 grant 2010/51884-8 Brazil
CitationJournal: Sci Rep / Year: 2017
Title: Crystal Structure of MpPR-1i, a SCP/TAPS protein from Moniliophthora perniciosa, the fungus that causes Witches' Broom Disease of Cacao.
Authors: Baroni, R.M. / Luo, Z. / Darwiche, R. / Hudspeth, E.M. / Schneiter, R. / Pereira, G.A.G. / Mondego, J.M.C. / Asojo, O.A.
History
DepositionMar 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR-1 protein
B: PR-1 protein
C: PR-1 protein
D: PR-1 protein
E: PR-1 protein
F: PR-1 protein
G: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)137,1967
Polymers137,1967
Non-polymers00
Water1,36976
1
A: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)19,5991
Polymers19,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)19,5991
Polymers19,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)19,5991
Polymers19,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)19,5991
Polymers19,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)19,5991
Polymers19,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)19,5991
Polymers19,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PR-1 protein


Theoretical massNumber of molelcules
Total (without water)19,5991
Polymers19,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.304, 84.085, 130.882
Angle α, β, γ (deg.)90.00, 111.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PR-1 protein


Mass: 19599.422 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moniliophthora perniciosa (fungus) / Gene: PR-1i / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: H6U756
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAuthors state that C-terminal sequence VRVPSLALLNLDLTTPFCNLPVNGSNDLDIR is the last exon which has ...Authors state that C-terminal sequence VRVPSLALLNLDLTTPFCNLPVNGSNDLDIR is the last exon which has not been included in UniProt H6U756.

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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: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8 M sodium formate, 70 mM Bis-Tris propane pH7.0, 21 mM zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 80587 / % possible obs: 99.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.036 / Net I/σ(I): 18.9
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.428 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7964 / CC1/2: 0.891 / Rpim(I) all: 0.546 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V51

5v51


Resolution: 2.43→45.09 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.663 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24283 3913 4.9 %RANDOM
Rwork0.20148 ---
obs0.20343 76657 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 86.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å23.55 Å2
2--4.5 Å2-0 Å2
3----4.89 Å2
Refinement stepCycle: 1 / Resolution: 2.43→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7357 0 0 76 7433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027574
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.8910342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7945929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16525.206413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.072151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6621536
X-RAY DIFFRACTIONr_chiral_restr0.1120.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216051
X-RAY DIFFRACTIONr_gen_planes_other
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_it18.4917.2883736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it21.06132.2694657
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it21.00317.5333838
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined25.23672.72932359
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: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 260 -
Rwork0.444 5498 -
obs--96.77 %

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