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- PDB-1uv7: periplasmic domain of EpsM from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 1uv7
Titleperiplasmic domain of EpsM from Vibrio cholerae
ComponentsGENERAL SECRETION PATHWAY PROTEIN M
KeywordsTRANSPORT / GENERAL SECRETION PATHWAY / VIBRIO CHOLERAE
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / : / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Type II secretion system protein GspM / Type II secretion system protein GspM, periplasmic domain superfamily / Type II secretion system (T2SS), protein M / General secretion pathway protein M, EpsM / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system protein M
Similarity search - Component
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsAbendroth, J. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of the Periplasmic Domain of the Type II Secretion System Protein Epsm from Vibrio Cholerae: The Simplest Version of the Ferredoxin Fold
Authors: Abendroth, J. / Rice, A. / Mcluskey, K. / Bagdasarian, M. / Hol, W.G.J.
History
DepositionJan 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENERAL SECRETION PATHWAY PROTEIN M
B: GENERAL SECRETION PATHWAY PROTEIN M


Theoretical massNumber of molelcules
Total (without water)25,2802
Polymers25,2802
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.879, 52.879, 112.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.60938, -0.79177, 0.04179), (-0.792, 0.6054, -0.07888), (0.03716, -0.08117, -0.99601)
Vector: 78.71606, 39.90469, 18.97545)

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Components

#1: Protein GENERAL SECRETION PATHWAY PROTEIN M / CHOLERA TOXIN SECRETION PROTEIN EPSM


Mass: 12639.798 Da / Num. of mol.: 2 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 65-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PET21D(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41851
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREQUIRED FOR SECRETION OF CHOLERA TOXIN THROUGH THE OUTER MEMBRANE.
Sequence detailsRESIDUES 166 TO 173 IN THE SEQRES RECORDS GIVEN BELOW ARE FROM THE HIS-TAG USED FOR THE EXPRESSION ...RESIDUES 166 TO 173 IN THE SEQRES RECORDS GIVEN BELOW ARE FROM THE HIS-TAG USED FOR THE EXPRESSION OF THE PROTEIN. RESIDUE 64 IS THE INITIAL EXPRESSION METHIONINE RESIDUE.

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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: 1.8 Å3/Da / Density % sol: 32.4 %
Crystal growTemperature: 277 K / pH: 8
Details: 6-12MG/ML PROTEIN IN 20MM TRIS PH8, 150MM NACL, 1MM TCEP; RESERVOIR: 2.4-3.0M SODIUM MALONATE, 100MM TRIS PH~8; CRYSTALLISATION: 1.5MKL PROTEIN + 1.5MKL RESERVIOR, 4C, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9791,0.9795,0.9686
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97951
30.96861
ReflectionResolution: 1.7→15.29 Å / Num. obs: 20676 / % possible obs: 99.7 % / Redundancy: 6.61 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 18
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.6 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.489 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERM 65-85 DISORDERED, LOOP 149-152 DISORDERED, HIS6-TAG DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1027 5 %RANDOM
Rwork0.196 ---
obs-19604 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å20 Å2
2---0.42 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 0 70 1298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221262
X-RAY DIFFRACTIONr_bond_other_d0.0020.021216
X-RAY DIFFRACTIONr_angle_refined_deg2.3021.9481704
X-RAY DIFFRACTIONr_angle_other_deg1.06832820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4695146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1580.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
X-RAY DIFFRACTIONr_nbd_refined0.2340.2236
X-RAY DIFFRACTIONr_nbd_other0.2530.21415
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.2885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.521.5750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.721232
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7063512
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9264.5472
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 62
Rwork0.262 1410
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)
15.23730.885-2.69845.43392.98327.0751-0.0268-0.10020.32890.0729-0.05850.62170.0438-0.43460.08530.03970.00490.03760.12420.02290.124828.0124.960316.6642
25.41773.37340.36366.4544-2.30035.6229-0.29420.33920.0964-0.34220.2726-0.0987-0.30540.33890.02160.1114-0.07790.03830.0722-0.01360.022942.356731.46741.27
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 165
2X-RAY DIFFRACTION2B86 - 163

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