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- PDB-2x9c: Crystal structure of a soluble PrgI mutant from Salmonella Typhimurium -

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Basic information

Entry
Database: PDB / ID: 2x9c
TitleCrystal structure of a soluble PrgI mutant from Salmonella Typhimurium
ComponentsPROTEIN PRGI
KeywordsPROTEIN TRANSPORT / NEEDLE PROTOMER / BACTERIAL PATHOGENESIS
Function / homologyType III secretion system, needle protein / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / go:0008565: / pathogenesis / identical protein binding / Protein PrgI
Function and homology information
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPoyraz, O. / Schmidt, H. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thuenemann, A.F. / Zychlinsky, A. / Baldus, M. / Lange, A. / Griesinger, C. / Kolbe, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Protein Refolding is Required for Assembly of the Type Three Secretion Needle
Authors: Poyraz, O. / Schmidt, H. / Seidel, K. / Delissen, F. / Ader, C. / Tenenboim, H. / Goosmann, C. / Laube, B. / Thuenemann, A.F. / Zychlinsky, A. / Baldus, M. / Lange, A. / Griesinger, C. / Kolbe, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 15, 2010 / Release: Jun 16, 2010
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 16, 2010Structure modelrepositoryInitial release
1.1May 26, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3May 8, 2019Structure modelData collection / Experimental preparation / Otherdatabase_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status_exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN PRGI
B: PROTEIN PRGI


Theoretical massNumber of molelcules
Total (without water)18,1822
Polymers18,1822
Non-polymers00
Water1629
1
A: PROTEIN PRGI


Theoretical massNumber of molelcules
Total (without water)9,0911
Polymers9,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN PRGI


Theoretical massNumber of molelcules
Total (without water)9,0911
Polymers9,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)64.530, 64.530, 104.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9934, -0.09595, 0.06291), (-0.09102, -0.99286, -0.07703), (0.06985, 0.0708, -0.99504)
Vector: 0.23139, -36.50947, 34.94272)

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Components

#1: Protein/peptide PROTEIN PRGI / PRGI


Mass: 9091.037 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: SL1344 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P41784
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O / Water
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 65 TO ALA ENGINEERED RESIDUE IN CHAIN A, VAL 67 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, VAL 65 TO ALA ENGINEERED RESIDUE IN CHAIN A, VAL 67 TO ALA ENGINEERED RESIDUE IN CHAIN B, VAL 65 TO ALA ENGINEERED RESIDUE IN CHAIN B, VAL 67 TO ALA

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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: 3.45 Å3/Da / Density % sol: 64.4 %
Description: DATA DETWINNED USING CNS WITH TWIN FRACTION 0.18 AND TWIN OPERATOR K,H,-L
Crystal growMethod: vapor diffusion, hanging drop
Details: RESERVOIR SOLUTION 0.15 MM NAH2PO4. SAMPLE BUFFER 20 MM HEPES (PH 7.5) 50 MM NACL. HANGING DROP WITH 1 UL SAMPLE AND 1 UL RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 11435 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.83
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.11 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.21refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CA5
Resolution: 2.45→38.13 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2660057.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CHAIN A RESIDUES 1-18 AND 80 ARE DISORDERED. CHAIN B RESIDUES 1-17 ARE DISORDERED. N-TERMINAL RESIDUES GLY-SER-HIS REMAINING FROM THROMBIN CLEAVAGE SITE ARE DISORDERED IN CHAINS A AND B. THE STRUCTURE WAS REFINED AT LOWER RESOLUTION (2.45 A) THAN THE COLLECTED DATASET (2.25 A) BECAUSE OF THE POOR MERGING STATISTICS AT HIGH RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 400 4.7 %RANDOM
Rwork0.225 ---
Obs0.225 8544 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.6715 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 81.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.8 Å20 Å20 Å2
2---7.8 Å20 Å2
3---15.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.45→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 0 9 967
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg1.1
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d17
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d0.69
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it1.832
c_mcangle_it3.033
c_scbond_it5.514.5
c_scangle_it7.656
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.071 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.542 59 4.1 %
Rwork0.439 1385 -
Obs--93.5 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PROTEIN_REP.PARAMPROTEIN.TOP
2WATER_REP.PARAMWATER.TOP

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