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- PDB-3h3m: Crystal structure of flagellar protein FliT from Bordetella bronc... -

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Basic information

Entry
Database: PDB / ID: 3h3m
TitleCrystal structure of flagellar protein FliT from Bordetella bronchiseptica
ComponentsFlagellar protein FliT
KeywordsSTRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Flagellum
Function / homology
Function and homology information


Flagellar protein flit. / Flagellar protein FliT / Flagellar protein FliT / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
UNKNOWN / Flagellar protein FliT / Flagellar protein FliT
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShumilin, I.A. / Wang, S. / Chruszcz, M. / Xu, X. / Le, B. / Cui, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of flagellar protein FliT from Bordetella bronchiseptica
Authors: Shumilin, I.A. / Wang, S. / Chruszcz, M. / Xu, X. / Le, B. / Cui, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar protein FliT
B: Flagellar protein FliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7283
Polymers28,6252
Non-polymers1031
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-32 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.751, 67.751, 82.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Flagellar protein FliT


Mass: 14312.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB2593, fliT / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Gold (de3) / References: UniProt: Q7WJA6, UniProt: A0A0H3LVQ9*PLUS
#2: Chemical ChemComp-UNK / UNKNOWN


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M POTASSIUM THIOCYANATE,30% PEG 2K MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2009 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→41.4 Å / Num. obs: 6894 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 18.939
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.512 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
REFMAC5.5.0089refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→41.4 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 21.502 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.566 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.271 326 4.7 %RANDOM
Rwork0.222 ---
obs0.225 6875 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 1 10 1306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221310
X-RAY DIFFRACTIONr_bond_other_d0.0040.02861
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9891779
X-RAY DIFFRACTIONr_angle_other_deg1.02932101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44323.92956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.30715220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.3521512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
X-RAY DIFFRACTIONr_mcbond_it0.8711.5853
X-RAY DIFFRACTIONr_mcbond_other0.1451.5342
X-RAY DIFFRACTIONr_mcangle_it1.67521353
X-RAY DIFFRACTIONr_scbond_it2.7263457
X-RAY DIFFRACTIONr_scangle_it4.1384.5426
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 21 -
Rwork0.229 469 -
obs--98.2 %
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)
12.7956-0.30531.02070.5766-0.37731.84450.2444-0.0242-0.39520.1505-0.120.17330.3953-0.408-0.12430.3057-0.02890.00240.3881-0.06270.34634.2847.54742.809
213.32335.6346-6.28567.6278-3.20136.2290.4062-0.38790.66740.3173-0.05080.3861-0.4516-0.2711-0.35540.20670.086-0.03440.2923-0.01640.170233.08958.53943.648
35.20381.17150.78213.8562-0.49582.06560.0924-0.69020.54320.323-0.25530.1673-0.39810.03380.16290.31790.0355-0.07570.3856-0.03810.300427.24364.16336.919
414.60553.1767-3.70592.3938-0.73073.66830.28690.3678-0.04430.0579-0.12940.01820.0474-0.2022-0.15740.1570.0154-0.02570.10820.0060.100831.57554.59835.079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 64
2X-RAY DIFFRACTION2A69 - 106
3X-RAY DIFFRACTION3B19 - 62
4X-RAY DIFFRACTION4B69 - 106

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