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- PDB-5v51: Crystal Structure of MpPR-1i Soaked with Selenourea for 10 min -

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Basic information

Entry
Database: PDB / ID: 5v51
TitleCrystal Structure of MpPR-1i Soaked with Selenourea for 10 min
ComponentsPR-1 protein
KeywordsLIPID BINDING PROTEIN / pathogenesis-related protein 1 / Cacao infection / selenourea
Function / homologySCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / selenourea / PR-1 protein
Function and homology information
Biological speciesMoniliophthora perniciosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.92 Å
AuthorsLuo, Z. / Asojo, O.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)SMOLBnet 2.0 grant 2010/51884-8 Brazil
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Crystal Structure of Moniliophthora perniciosa Pathogenesis Related protein 1i phased by selenourea
Authors: Luo, Z. / Asojo, O. / Mondego, J.
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.country / _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,30316
Polymers137,1967
Non-polymers1,1079
Water00
1
A: PR-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7222
Polymers19,5991
Non-polymers1231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PR-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7222
Polymers19,5991
Non-polymers1231
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PR-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7222
Polymers19,5991
Non-polymers1231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PR-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7222
Polymers19,5991
Non-polymers1231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PR-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8453
Polymers19,5991
Non-polymers2462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PR-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9684
Polymers19,5991
Non-polymers3693
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.412, 81.905, 130.238
Angle α, β, γ (deg.)90.00, 111.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEGLYGLYAA32 - 16310 - 141
21PHEPHEGLYGLYBB32 - 16310 - 141
12PHEPHETYRTYRAA32 - 15910 - 137
22PHEPHETYRTYRCC32 - 15910 - 137
13PHEPHEASNASNAA32 - 16110 - 139
23PHEPHEASNASNDD32 - 16110 - 139
14PHEPHEGLYGLYAA32 - 16310 - 141
24PHEPHEGLYGLYEE32 - 16310 - 141
15PHEPHEALAALAAA32 - 16210 - 140
25PHEPHEALAALAFF32 - 16210 - 140
16PHEPHEGLYGLYAA32 - 16310 - 141
26PHEPHEGLYGLYGG32 - 16310 - 141
17PHEPHETYRTYRBB32 - 15910 - 137
27PHEPHETYRTYRCC32 - 15910 - 137
18PHEPHEASNASNBB32 - 16110 - 139
28PHEPHEASNASNDD32 - 16110 - 139
19PHEPHEGLYGLYBB32 - 16310 - 141
29PHEPHEGLYGLYEE32 - 16310 - 141
110PHEPHEALAALABB32 - 16210 - 140
210PHEPHEALAALAFF32 - 16210 - 140
111PHEPHEGLYGLYBB32 - 16310 - 141
211PHEPHEGLYGLYGG32 - 16310 - 141
112PHEPHETYRTYRCC32 - 15910 - 137
212PHEPHETYRTYRDD32 - 15910 - 137
113PHEPHETYRTYRCC32 - 15910 - 137
213PHEPHETYRTYREE32 - 15910 - 137
114PHEPHETYRTYRCC32 - 15910 - 137
214PHEPHETYRTYRFF32 - 15910 - 137
115PHEPHETYRTYRCC32 - 15910 - 137
215PHEPHETYRTYRGG32 - 15910 - 137
116PHEPHEASNASNDD32 - 16110 - 139
216PHEPHEASNASNEE32 - 16110 - 139
117GLNGLNASNASNDD31 - 1619 - 139
217GLNGLNASNASNFF31 - 1619 - 139
118PHEPHEASNASNDD32 - 16110 - 139
218PHEPHEASNASNGG32 - 16110 - 139
119PHEPHEALAALAEE32 - 16210 - 140
219PHEPHEALAALAFF32 - 16210 - 140
120PHEPHEGLYGLYEE32 - 16310 - 141
220PHEPHEGLYGLYGG32 - 16310 - 141
121PHEPHEALAALAFF32 - 16210 - 140
221PHEPHEALAALAGG32 - 16210 - 140

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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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: Chemical
ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH4N2Se
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: 3.92 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8 M sodium formate, 70 mM Bis-Tris prooane 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: 2.9→50 Å / Num. obs: 46260 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.046 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4495 / CC1/2: 0.867 / Rpim(I) all: 0.471 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.92→45.07 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.558 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.844 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22835 1814 5.2 %RANDOM
Rwork0.18711 ---
obs0.18922 33097 74.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å20.59 Å2
2--1.13 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.92→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7279 0 36 0 7315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.88810261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1335916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8825.135407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.097151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.2161536
X-RAY DIFFRACTIONr_chiral_restr0.10.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216015
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_it10.20514.0153688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it14.78126.1894596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.66414.653834
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined20.81959.75531610
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A3260.1
12B3260.1
21A2940.06
22C2940.06
31A3120.17
32D3120.17
41A3260.14
42E3260.14
51A3360.08
52F3360.08
61A3360.1
62G3360.1
71B2900.11
72C2900.11
81B3240.13
82D3240.13
91B3300.13
92E3300.13
101B3460.12
102F3460.12
111B3360.13
112G3360.13
121C2960.16
122D2960.16
131C2900.08
132E2900.08
141C2980.08
142F2980.08
151C2880.07
152G2880.07
161D3260.16
162E3260.16
171D3260.15
172F3260.15
181D3120.16
182G3120.16
191E3280.12
192F3280.12
201E3320.16
202G3320.16
211F3540.08
212G3540.08
LS refinement shellResolution: 2.917→2.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 58 -
Rwork0.344 882 -
obs--27.61 %

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