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- PDB-4g54: Crystal structure of a periplasmic domain of the EpsAB fusion pro... -

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Basic information

Entry
Database: PDB / ID: 4g54
TitleCrystal structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system
ComponentsGeneral Secretion Pathway Protein
KeywordsPeptidoglycan-binding protein / Type 2 Secretion System protein
Function / homology
Function and homology information


type II protein secretion system complex
Similarity search - Function
Type II secretion system protein GspB / Type II secretion system protein B / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / AAA domain / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Cysteine proteinases ...Type II secretion system protein GspB / Type II secretion system protein B / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / AAA domain / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Cysteine proteinases / Cathepsin B; Chain A / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
General secretion pathway protein A
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsMartynnowski, D. / Grochulski, P. / Howard, S.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system.
Authors: Martynowski, D. / Grochulski, P. / Howard, P.S.
History
DepositionJul 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General Secretion Pathway Protein


Theoretical massNumber of molelcules
Total (without water)29,8671
Polymers29,8671
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.821, 44.523, 51.040
Angle α, β, γ (deg.)90.00, 110.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein General Secretion Pathway Protein


Mass: 29867.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio vulnificus (bacteria) / References: UniProt: A0A3Q0L2C6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 220 mM Calcium Chloride, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 87 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 28, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 35030 / Num. obs: 36885 / % possible obs: 93 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.55→1.59 Å / % possible all: 93.2

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Processing

Software
NameVersionClassification
MsDCdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→47.78 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.034 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20223 1851 5 %RANDOM
Rwork0.1747 ---
obs0.17615 35030 93.19 %-
all-36885 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 0 253 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3071.9622542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73223.40494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51915334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3751520
X-RAY DIFFRACTIONr_chiral_restr0.1820.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211415
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_it1.411.51111
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47221800
X-RAY DIFFRACTIONr_scbond_it4.023759
X-RAY DIFFRACTIONr_scangle_it6.614.5742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 83 -
Rwork0.342 1540 -
obs--55.83 %
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)
13.343-0.9470.89111.3955-0.46071.8827-0.00070.2829-0.1584-0.164-0.0016-0.05840.2036-0.00780.00230.1036-0.01140.0210.0964-0.01350.029421.9531-8.2065-4.5674
21.9939-0.52410.86790.9418-0.24391.1959-0.058-0.1563-0.02770.01370.0570.01920.1234-0.20310.00090.0645-0.0150.0080.1011-0.00110.052416.8816-3.77897.5315
35.1408-1.36820.02072.27010.36291.86450.080.2318-0.3478-0.2087-0.10720.22520.1516-0.26340.02720.0628-0.0355-0.01720.1262-0.01820.056510.4694-4.6171-3.9313
42.6869-0.21970.82071.5192-0.26371.10230.00450.22020.049-0.0879-0.00420.10190.064-0.199-0.00030.0333-0.018-0.00040.13150.00020.051810.3298-0.8959-5.3375
50.4402-0.03030.18131.5220.53470.8831-0.00040.01020.0165-0.01980.0357-0.0954-0.01940.0388-0.03530.0734-0.0020.00720.04730.00210.072227.17186.174621.3149
66.25474.4125-5.153.2931-4.878512.9832-0.1190.40071.0055-0.09790.38970.6422-0.0319-0.7099-0.27070.1005-0.069-0.00080.13110.07330.277224.052510.4242-5.6004
71.4750.09892.43850.34421.05656.5165-0.13310.19590.21880.02760.1054-0.1441-0.04570.52550.02770.0709-0.02760.02110.11320.00320.194233.2678-1.2043.0357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A343 - 377
2X-RAY DIFFRACTION2A378 - 404
3X-RAY DIFFRACTION3A405 - 425
4X-RAY DIFFRACTION4A426 - 453
5X-RAY DIFFRACTION5A454 - 531
6X-RAY DIFFRACTION6A532 - 550
7X-RAY DIFFRACTION7A551 - 570

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