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- PDB-4err: 1.55 Angstrom Crystal Structure of the Four Helical Bundle Membra... -

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Entry
Database: PDB / ID: 4err
Title1.55 Angstrom Crystal Structure of the Four Helical Bundle Membrane Localization Domain (4HBM) of the Vibrio vulnificus MARTX Effector Domain DUF5
ComponentsAutotransporter adhesin
KeywordsPROTEIN BINDING / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / four helical bundle membrane localization domain
Function / homology
Function and homology information


host cell cytosol / peptidase activity / toxin activity / transferase activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
: / : / Pasteurella multocida toxin, C2 domain / C-terminal repeat from RTX toxins / : / RtxA toxin / RtxA repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain ...: / : / Pasteurella multocida toxin, C2 domain / C-terminal repeat from RTX toxins / : / RtxA toxin / RtxA repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Serine aminopeptidase, S33 / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serine aminopeptidase, S33 / Serralysin-like metalloprotease, C-terminal / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Autotransporter adhesin / Autotransporter adhesin
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMinasov, G. / Wawrzak, Z. / Geissler, B. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Satchell, K.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.55 Angstrom Crystal Structure of the Four Helical Bundle Membrane Localization Domain (4HBM) of the Vibrio vulnificus MARTX Effector Domain DUF5.
Authors: Minasov, G. / Wawrzak, Z. / Geissler, B. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Satchell, K.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

Downloads & links

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Assembly

Deposited unit
A: Autotransporter adhesin
B: Autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5346
Polymers20,3032
Non-polymers2314
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-50 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.896, 49.874, 72.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Autotransporter adhesin


Mass: 10151.451 Da / Num. of mol.: 2 / Fragment: Effector Domain DUF5 (UNP residues 3591-3669)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV2_0479 / Plasmid: pYCpet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8D6P9, UniProt: A0A3Q0KY79*PLUS
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 13mG/mL, 0.1M Sodium chloride, TRIS-HCl pH 7.0, 6.9 mM Phosphatidylserine (PS); Screen: JCSG+ (G10), 0.15M Potassium bromide, 30% w/v PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 24039 / Num. obs: 24039 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.7
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1175 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EBF

2ebf


Resolution: 1.55→29.22 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.576 / SU ML: 0.059
Isotropic thermal model: Thermal Factors Anisotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1223 5.1 %RANDOM
Rwork0.16717 ---
all0.16983 22766 --
obs0.16983 22766 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.373 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0 Å2
2--1.19 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 4 239 1528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221538
X-RAY DIFFRACTIONr_bond_other_d0.0010.021065
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9682098
X-RAY DIFFRACTIONr_angle_other_deg0.85232651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6715211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11426.43873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.595156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02283
X-RAY DIFFRACTIONr_mcbond_it1.971.5963
X-RAY DIFFRACTIONr_mcbond_other0.8281.5386
X-RAY DIFFRACTIONr_mcangle_it3.26821573
X-RAY DIFFRACTIONr_scbond_it4.423575
X-RAY DIFFRACTIONr_scangle_it6.5324.5525
X-RAY DIFFRACTIONr_rigid_bond_restr1.06312603
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 75 -
Rwork0.297 1607 -
obs-1607 96 %
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)
11.93670.1398-0.75130.19170.1991.0218-0.04930.3136-0.0751-0.02010.04020.0058-0.0039-0.12770.00920.021-0.0110.00640.0868-0.01170.030319.346130.775425.3372
20.5429-0.0219-0.38010.0825-0.11890.69480.020.03590.02410.0070.00970.007-0.0152-0.0376-0.02980.0208-0.0010.00180.0425-0.00010.030115.866133.166535.3124
30.02490.03-0.13440.0725-0.0411.21420.0206-0.00320.00680.0205-0.0070.0157-0.0706-0.0022-0.01360.0358-0.00320.00320.0392-0.0010.033414.797733.727859.8278
40.16310.1175-0.41340.1421-0.16051.3848-0.0045-0.00180.0022-0.0003-0.00350.00460.0374-0.00830.00790.0237-0.0018-0.00290.0413-0.00080.032414.095424.81163.3124
50.97440.58850.18650.36630.19230.6985-0.03180.1192-0.1815-0.02440.0866-0.1128-0.01480.0479-0.05480.02-0.0070.00980.0558-0.02370.061921.147822.916432.2725
61.23490.7123-1.08310.4625-0.63890.9540.2092-0.3280.06390.0729-0.15040.0558-0.1680.2784-0.05880.079-0.0772-0.00510.1368-0.01450.030725.625431.821165.6468
71.7910.2357-1.34350.107-0.38431.57570.1434-0.1730.14540.0329-0.0370.0203-0.14980.1806-0.10650.0503-0.02930.00870.0612-0.01330.045528.884434.2155.5102
80.56330.0479-0.13930.0348-0.15450.7546-0.00550.021-0.02360.00610.0004-0.0078-0.01790.03270.00510.0236-0.00430.00160.04120.00040.033929.992932.969931.3467
90.515-0.2007-0.67830.22980.1371.7761-0.08240.0871-0.09550.0149-0.06620.00690.1126-0.06020.14870.0195-0.00560.010.0486-0.01120.051330.867823.976928.5455
102.2294-0.1723-0.68940.01370.00557.2676-0.0055-0.204-0.1863-0.00250.01640.01530.27510.0318-0.01090.0229-0.0084-0.00510.04920.01150.050323.724523.562759.9677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3590 - 3595
2X-RAY DIFFRACTION2A3596 - 3606
3X-RAY DIFFRACTION3A3607 - 3627
4X-RAY DIFFRACTION4A3628 - 3650
5X-RAY DIFFRACTION5A3651 - 3671
6X-RAY DIFFRACTION6B3590 - 3595
7X-RAY DIFFRACTION7B3596 - 3606
8X-RAY DIFFRACTION8B3607 - 3627
9X-RAY DIFFRACTION9B3628 - 3650
10X-RAY DIFFRACTION10B3651 - 3672

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