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- PDB-4lgo: Crystal Structure of N-terminal domain 1 of VompD from Bartonella... -

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Basic information

Entry
Database: PDB / ID: 4lgo
TitleCrystal Structure of N-terminal domain 1 of VompD from Bartonella quintana
ComponentsVompD
KeywordsCELL ADHESION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / trimeric autotransporter adhesin / autotransporter adhesin / outer membrane
Function / homology
Function and homology information


cell outer membrane / cell surface
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Surface protein/Bartonella adhesin / VompD
Similarity search - Component
Biological speciesBartonella quintana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of N-terminal domain 1 of VompD from Bartonella quintana
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 20, 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: VompD
B: VompD
C: VompD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9955
Polymers43,8713
Non-polymers1242
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-109 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.030, 37.110, 109.780
Angle α, β, γ (deg.)90.000, 119.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

21B-583-

HOH

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Components

#1: Protein VompD


Mass: 14623.595 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: vompD / Production host: Escherichia coli (E. coli) / References: UniProt: Q64HT0, UniProt: A0A0H3LUZ2*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: Wizard3/4_b12: 2M Ammonium Sulfate, 0.1M Sodium Acetate/HCl, pH=4.6, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2013 / Details: beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 46989 / Num. obs: 46707 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 30.647 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 20.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.4812.7212835344699.8
1.74-1.790.3963.3112371331499.7
1.79-1.840.2774.7212249328299.8
1.84-1.90.2126.2311775315399.7
1.9-1.960.1538.4311512308199.5
1.96-2.030.11211.1111079295999.7
2.03-2.110.08614.1210689285199.7
2.11-2.190.07316.3310373276699.7
2.19-2.290.06318.699921264499.5
2.29-2.40.05321.89590256099.5
2.4-2.530.04525.258958238199.4
2.53-2.690.03929.188650230299.5
2.69-2.870.03333.568072215799
2.87-3.10.02938.797482200399.4
3.1-3.40.02444.846911185199
3.4-3.80.02249.266218167599.2
3.8-4.390.02151.315485148098.7
4.39-5.380.0253.944657127098.3
5.38-7.60.0252.253594100698.8
7.60.01853.02175552689.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D9X

3d9x


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.512 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 2364 5.1 %RANDOM
Rwork0.1668 ---
all0.1679 46989 --
obs0.1679 46707 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.35 Å2 / Biso mean: 30.409 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.44 Å2
2--2.71 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 8 281 2870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192630
X-RAY DIFFRACTIONr_bond_other_d0.0010.022596
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9353562
X-RAY DIFFRACTIONr_angle_other_deg0.73635936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.78827.686121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37115454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.898158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_mcbond_it1.1181.4521417
X-RAY DIFFRACTIONr_mcbond_other1.1181.451416
X-RAY DIFFRACTIONr_mcangle_it1.8752.1631768
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 166 -
Rwork0.258 3270 -
all-3436 -
obs--99.85 %
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)
11.5927-0.17910.45870.6320.30044.01530.1295-0.3410.1869-0.01070.07170.0249-0.4342-0.5393-0.20120.08860.04690.03720.1456-0.0140.141816.938812.844861.3039
20.4782-0.2031-0.81970.2355-0.15544.49690.03420.0582-0.03-0.06490.0130.09410.2076-0.146-0.04710.0835-0.0178-0.02520.0398-0.00210.126926.13884.722631.8344
31.19111.1529-1.57554.82563.22098.2202-0.02150.1335-0.039-0.30760.0191-0.1005-0.198-0.29460.00240.21160.0719-0.03150.10870.00270.085930.52987.40132.953
41.71080.03081.64762.587-1.983523.31570.2511-0.3444-0.21910.21030.35040.13930.7768-1.3286-0.60150.0885-0.0945-0.01010.47170.09710.16594.74642.339965.8048
50.6508-0.0785-0.37490.1138-0.01753.9930.02660.0155-0.0238-0.02570.03940.02320.2462-0.3664-0.0660.0696-0.0177-0.02950.0496-0.00130.134922.93773.771140.8003
61.23490.146-0.10175.7532-4.45639.48520.02010.3538-0.0857-0.36170.0547-0.0670.14920.3536-0.07480.10740.0434-0.00120.1821-0.01790.02238.01867.55915.1752
75.72610.2093-1.88935.471-0.984310.79130.0845-0.62960.24440.10460.15720.2503-0.698-0.5104-0.24170.12640.1440.05510.2874-0.02440.189610.998118.680564.3544
81.51340.0705-0.29850.2924-0.52274.69760.1308-0.06910.04480.00590.18420.10310.0475-0.916-0.3150.0178-0.0151-0.00960.22250.06960.121412.08256.059248.9107
91.66670.11640.05961.16430.8954.09080.0480.3169-0.0453-0.1338-0.00690.03490.24080.1478-0.04110.11580.0288-0.02570.0854-0.00330.0532.33034.261813.508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A223 - 268
2X-RAY DIFFRACTION2A269 - 321
3X-RAY DIFFRACTION3A322 - 339
4X-RAY DIFFRACTION4B223 - 238
5X-RAY DIFFRACTION5B239 - 322
6X-RAY DIFFRACTION6B323 - 338
7X-RAY DIFFRACTION7C223 - 233
8X-RAY DIFFRACTION8C234 - 294
9X-RAY DIFFRACTION9C295 - 339

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