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- PDB-3opc: Crystal structure of FlgN chaperone from Bordetella pertussis -

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Basic information

Entry
Database: PDB / ID: 3opc
TitleCrystal structure of FlgN chaperone from Bordetella pertussis
ComponentsUncharacterized protein
KeywordsCHAPERONE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / FLAGELLUM BIOSYNTHESIS
Function / homologyFlgN-like / FlgN-like protein / FlgN-like superfamily / FlgN protein / bacterial-type flagellum assembly / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Flagellar protein FlgN
Function and homology information
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsMichalska, K. / Chhor, G. / Bearden, J. / Fenske, R.J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of FlgN chaperone from Bordetella pertussis
Authors: Michalska, K. / Chhor, G. / Bearden, J. / Fenske, R.J. / Joachimiak, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4493
Polymers32,3572
Non-polymers921
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-73 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.57, 90.39, 49.19
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein


Mass: 16178.491 Da / Num. of mol.: 2 / Fragment: Sequence database residues 1-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / Gene: BP1370, FlgN / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, pRK1037 / References: UniProt: Q7VYH2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 46.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M MgCl2, 0.1 M HEPES, 22% polyacrylic acid 5100 sodium salt, strontium chloride 0.01 M, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924, 0.9793992, 0.9796705
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.97939921
30.97967051
ReflectionResolution: 2.09→50 Å / Num. obs: 18169 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.4 / Num. unique all: 900 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
Auto-Rickshawphasing
SHELXDphasing
ABSmodel building
SHARPphasing
DMmodel building
HELICAPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
ABSphasing
DMphasing
HELICAPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.09→27.45 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.893 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25574 1297 7.2 %RANDOM
Rwork0.21306 ---
all0.21601 18056 --
obs0.21601 18056 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---1.9 Å20 Å2
3---2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.09→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 6 84 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212028
X-RAY DIFFRACTIONr_bond_other_d0.0010.021337
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9542750
X-RAY DIFFRACTIONr_angle_other_deg0.86533255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3035270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7324.423104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4311522
X-RAY DIFFRACTIONr_chiral_restr0.0650.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_mcbond_it0.6891.51330
X-RAY DIFFRACTIONr_mcbond_other0.171.5539
X-RAY DIFFRACTIONr_mcangle_it1.34622082
X-RAY DIFFRACTIONr_scbond_it2.53698
X-RAY DIFFRACTIONr_scangle_it4.2564.5668
LS refinement shellResolution: 2.091→2.145 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 105 -
Rwork0.253 1215 -
obs--98.36 %
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)
12.30751.73220.9751.97791.3610.73490.03770.0829-0.03380.09450.0903-0.04870.06290.0778-0.1280.1026-0.0328-0.01860.0987-0.0030.115748.932229.43115.7224
21.7521.24471.0631.71491.20290.5664-0.1660.35090.0371-0.23860.213-0.0247-0.14330.1532-0.0470.1473-0.0983-0.01130.1217-0.00830.05217.7447-3.57253.5804
32.20870.692-0.1650.3188-0.99793.10890.1113-0.0683-0.0367-0.00460.06620.08550.0255-0.2682-0.17750.0375-0.0233-0.03620.0964-0.00510.136-1.1105-22.52345.5561
41.29112.92810.16927.3360.80480.13950.0971-0.01280.14060.1897-0.07560.26450.04270.0027-0.02150.1025-0.029-0.00190.08740.00190.094614.9713-2.088615.6352
522.91076.299814.5042-6.84140.80124.0297-1.2342-1.0624-1.315-0.34440.31-0.45130.0712-1.02910.9242-0.0118-0.07140.2060.1199-0.410.80772.0055-29.8885-0.2276
60.50351.8860.55225.22181.76420.9741-0.03510.0712-0.0942-0.14710.1222-0.2074-0.08390.1074-0.08710.0655-0.01670.00060.0937-0.05440.139116.6274-13.93867.5111
71.44280.95420.3751.12260.66790.21030.066-0.00590.17930.1492-0.03970.03950.0626-0.0504-0.02630.1039-0.0484-0.00010.05530.00830.084246.077932.571418.4992
88.39464.20020.31222.4841-0.14540.11480.1110.40580.24210.15560.04630.2031-0.0755-0.0059-0.15730.0511-0.00710.00790.12810.04980.148429.596125.67769.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 33
2X-RAY DIFFRACTION2A34 - 62
3X-RAY DIFFRACTION3A63 - 83
4X-RAY DIFFRACTION4A84 - 128
5X-RAY DIFFRACTION5B-1 - 4
6X-RAY DIFFRACTION6B5 - 29
7X-RAY DIFFRACTION7B30 - 91
8X-RAY DIFFRACTION8B92 - 129

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