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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 / CAP superfamily / Cysteine-rich secretory protein family / 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

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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
Water0
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A32 - 163
2010B32 - 163
1020A32 - 159
2020C32 - 159
1030A32 - 161
2030D32 - 161
1040A32 - 163
2040E32 - 163
1050A32 - 162
2050F32 - 162
1060A32 - 163
2060G32 - 163
1070B32 - 159
2070C32 - 159
1080B32 - 161
2080D32 - 161
1090B32 - 163
2090E32 - 163
10100B32 - 162
20100F32 - 162
10110B32 - 163
20110G32 - 163
10120C32 - 159
20120D32 - 159
10130C32 - 159
20130E32 - 159
10140C32 - 159
20140F32 - 159
10150C32 - 159
20150G32 - 159
10160D32 - 161
20160E32 - 161
10170D31 - 161
20170F31 - 161
10180D32 - 161
20180G32 - 161
10190E32 - 162
20190F32 - 162
10200E32 - 163
20200G32 - 163
10210F32 - 162
20210G32 - 162

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 / Selenourea


Mass: 123.016 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH4N2Se
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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