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- PDB-5ziy: Crystal structure of Bacillus cereus FlgL -

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Basic information

Entry
Database: PDB / ID: 5ziy
TitleCrystal structure of Bacillus cereus FlgL
ComponentsFlagellar hook-associated protein 3
KeywordsSTRUCTURAL PROTEIN / flagellum / junction
Function / homologyFlagellar hook-associated protein 3 / bacterial-type flagellum hook / Bacterial flagellin C-terminal helical region / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / bacterial-type flagellum-dependent cell motility / structural molecule activity / Flagellar hook-associated protein 3
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsHong, H.J. / Kim, T.H. / Song, W.S. / Yoon, S.I.
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of FlgL and its implications for flagellar assembly
Authors: Hong, H.J. / Kim, T.H. / Song, W.S. / Ko, H.J. / Lee, G.S. / Kang, S.G. / Kim, P.H. / Yoon, S.I.
History
DepositionMar 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar hook-associated protein 3
B: Flagellar hook-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7139
Polymers47,2552
Non-polymers4587
Water1,58588
1
A: Flagellar hook-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0207
Polymers23,6271
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar hook-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6932
Polymers23,6271
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-88 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.619, 57.986, 67.914
Angle α, β, γ (deg.)90.00, 114.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEVALVALAA66 - 9528 - 57
21ILEILEVALVALBB66 - 9528 - 57
12ILEILELEULEUAA114 - 18576 - 147
22ILEILELEULEUBB114 - 18576 - 147
13LEULEULEULEUAA203 - 235165 - 197
23LEULEULEULEUBB203 - 235165 - 197

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Components

#1: Protein Flagellar hook-associated protein 3 / Flagellar hook-associated protein FlgL


Mass: 23627.332 Da / Num. of mol.: 2 / Fragment: UNP residues 45-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: flgL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A164TZ51
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% PEG 8000, 0.1M Hepes, pH 7.4, and 0.2M zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 23891 / % possible obs: 95.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 20.2
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1231

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.202 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24976 1214 5.1 %RANDOM
Rwork0.21244 ---
obs0.21441 22641 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 32.681 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å20 Å21.04 Å2
2--1.75 Å20 Å2
3---2.39 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 7 88 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222781
X-RAY DIFFRACTIONr_bond_other_d00.021768
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9593763
X-RAY DIFFRACTIONr_angle_other_deg4.39234375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.995364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27627.008127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29915483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.573158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023149
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02489
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_it0.5731.51816
X-RAY DIFFRACTIONr_mcbond_other01.5754
X-RAY DIFFRACTIONr_mcangle_it1.08122886
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1143965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6114.5877
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
797medium positional0.150.5
909loose positional0.355
797medium thermal0.572
909loose thermal0.7310
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 108 -
Rwork0.227 1674 -
obs--97.7 %
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)
117.41411.80624.58781.5130.87522.44760.20380.0691-0.89930.177-0.0453-0.18670.0861-0.1389-0.15850.31580.0047-0.05370.02470.00750.175921.966-5.629-2.376
26.32461.02581.25081.82530.10120.9773-0.04740.03250.20440.0146-0.0259-0.3109-0.07260.03470.07340.32670.0031-0.05110.02840.02370.104232.9656.7770.148
315.6767.20424.46375.26072.61862.07740.5561-0.5535-0.72790.6052-0.2801-0.29520.216-0.133-0.2760.33770.0057-0.07740.10590.09930.1725.825-5.5435.975
423.5561-1.90955.21991.2353-0.51664.12250.22541.7162-0.1128-0.1177-0.13050.04390.12220.1494-0.09480.3493-0.0015-0.0530.24530.01560.04329.4885.473-21.997
55.34260.2050.38191.5385-0.08743.6578-0.06250.23070.39340.03930.10590.18290.0585-0.4802-0.04350.3149-0.0107-0.04330.13330.03660.07871.89510.901-13.388
633.6517-8.4354-6.03433.90281.17544.24150.39631.2578-0.0067-0.2607-0.20920.3423-0.0654-0.0746-0.18710.3803-0.008-0.06980.43940.08680.08827.94712.438-26.028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 99
2X-RAY DIFFRACTION2A104 - 196
3X-RAY DIFFRACTION3A197 - 243
4X-RAY DIFFRACTION4B56 - 97
5X-RAY DIFFRACTION5B110 - 196
6X-RAY DIFFRACTION6B197 - 240

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