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- PDB-4mh6: 2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO... -

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Basic information

Entry
Database: PDB / ID: 4mh6
Title2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO from Vibrio parahaemolyticus
ComponentsPutative type III secretion protein YscO
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyType III secretion sytem,YscO / Type III secretion protein YscO / Helix Hairpins - #1700 / : / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / PHOSPHATE ION / Putative type III secretion protein YscO
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO from Vibrio parahaemolyticus.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative type III secretion protein YscO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5133
Polymers21,3231
Non-polymers1902
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.114, 149.114, 63.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-309-

HOH

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Components

#1: Protein Putative type III secretion protein YscO


Mass: 21322.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VP1669, yscO / Plasmid: pMCSG7 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Rosetta gami 2 / References: UniProt: Q87P49
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Protein: 2.28 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: JCSG+ (C9), 0.1M Sodium/Potasium phosphate pH 6.2, 25% (v/v) 1,2 Propanediol, 10% (v/v) Glycerol, VAPOR ...Details: Protein: 2.28 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: JCSG+ (C9), 0.1M Sodium/Potasium phosphate pH 6.2, 25% (v/v) 1,2 Propanediol, 10% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 9084 / Num. obs: 9084 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 10 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 4.2 / Num. unique all: 436 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
SHELXSphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.24 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 17.508 / SU ML: 0.187
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24308 434 4.8 %RANDOM
Rwork0.18946 ---
obs0.19195 8645 99.69 %-
all-8645 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å20 Å2
2--0.46 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 10 93 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191394
X-RAY DIFFRACTIONr_bond_other_d0.0010.021383
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9681869
X-RAY DIFFRACTIONr_angle_other_deg0.71833167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9355164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.1652586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60515294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8411516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021602
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02334
X-RAY DIFFRACTIONr_mcbond_it2.4962.644650
X-RAY DIFFRACTIONr_mcbond_other2.4682.635649
X-RAY DIFFRACTIONr_mcangle_it4.2623.951816
X-RAY DIFFRACTIONr_mcangle_other4.263.963817
X-RAY DIFFRACTIONr_scbond_it3.7593.149744
X-RAY DIFFRACTIONr_scbond_other3.5533.125737
X-RAY DIFFRACTIONr_scangle_other5.9174.5311042
X-RAY DIFFRACTIONr_long_range_B_refined8.7421.2181692
X-RAY DIFFRACTIONr_long_range_B_other8.6921.0861679
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 31 -
Rwork0.228 612 -
obs-612 98.62 %
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)
18.35040.3432-4.85599.06212.614914.35580.70540.0144-0.7250.6890.1062-0.042-0.49181.164-0.81160.1324-0.032-0.06370.3355-0.00440.331377.76367.43068.9547
215.9124-7.05146.99613.2442-3.36884.2698-0.0973-0.08490.4335-0.0259-0.0692-0.20640.00560.0890.16650.12320.0432-0.05890.11620.04240.129152.236480.4082-5.3292
33.5354-1.8370.56311.9311-2.31734.64560.08660.28190.1422-0.07450.0509-0.0046-0.0903-0.3926-0.13750.16440.0192-0.03590.20870.02190.062414.329697.7763-35.604
411.0964-8.664113.18627.1951-10.456215.7990.40880.50730.03-0.4613-0.498-0.26820.60070.52450.08930.2520.093-0.02620.33860.02860.19530.464986.7282-27.2686
522.3615-9.405619.88324.9004-7.065622.89740.545-0.6502-0.5451-0.32020.14640.30770.9523-0.4487-0.69140.1240.0456-0.07560.12530.06360.171259.407667.12114.3406
622.6848-10.772821.08688.7766-15.152426.84810.51180.4291-0.51560.82840.30420.4869-1.0102-0.1805-0.8160.42520.2599-0.05760.5411-0.03060.172777.761459.074525.0901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - -1
2X-RAY DIFFRACTION2A0 - 34
3X-RAY DIFFRACTION3A35 - 69
4X-RAY DIFFRACTION4A70 - 110
5X-RAY DIFFRACTION5A111 - 133
6X-RAY DIFFRACTION6A134 - 148

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