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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 / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding
Similarity search - Function
Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein
Similarity search - Domain/homology
SPI-1 type 3 secretion system needle filament protein
Similarity search - Component
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. ...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.
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.
History
DepositionMar 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
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 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
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

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 ...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
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.832
X-RAY DIFFRACTIONc_mcangle_it3.033
X-RAY DIFFRACTIONc_scbond_it5.514.5
X-RAY DIFFRACTIONc_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
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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