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- PDB-2j69: Bacterial dynamin-like protein BDLP -

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Basic information

Entry
Database: PDB / ID: 2j69
TitleBacterial dynamin-like protein BDLP
ComponentsBACTERIAL DYNAMIN-LIKE PROTEIN
KeywordsHYDROLASE / DYNAMIN / FZO / FZL / GTPASE
Function / homology
Function and homology information


dynamin GTPase / mitochondrial fusion / GTPase activity / lipid binding / GTP binding / identical protein binding / plasma membrane
Similarity search - Function
: / Bacterial dynamin-like protein, helical domain / Mitofusin family / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Bacterial dynamin-like protein
Similarity search - Component
Biological speciesNOSTOC PUNCTIFORME (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsLow, H.H. / Lowe, J.
CitationJournal: Nature / Year: 2006
Title: A Bacterial Dynamin-Like Protein
Authors: Low, H.H. / Lowe, J.
History
DepositionSep 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIAL DYNAMIN-LIKE PROTEIN
B: BACTERIAL DYNAMIN-LIKE PROTEIN
C: BACTERIAL DYNAMIN-LIKE PROTEIN
D: BACTERIAL DYNAMIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)314,8724
Polymers314,8724
Non-polymers00
Water00
1
A: BACTERIAL DYNAMIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)78,7181
Polymers78,7181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BACTERIAL DYNAMIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)78,7181
Polymers78,7181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BACTERIAL DYNAMIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)78,7181
Polymers78,7181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BACTERIAL DYNAMIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)78,7181
Polymers78,7181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)214.289, 218.596, 151.198
Angle α, β, γ (deg.)90.00, 134.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 695
2114B3 - 695
3114C3 - 695
4114D3 - 695

NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2given(1), (1), (1)
3given(1), (1), (1)
4given(1), (1), (1)

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Components

#1: Protein
BACTERIAL DYNAMIN-LIKE PROTEIN


Mass: 78717.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOSTOC PUNCTIFORME (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B2IZD3*PLUS

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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: 4.17 Å3/Da / Density % sol: 69 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 86547 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.886 / SU B: 40.373 / SU ML: 0.338 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.334 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 4869 5 %RANDOM
Rwork0.236 ---
obs0.238 92114 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 61.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å2-1.19 Å2
2--1.65 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21500 0 0 0 21500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02221788
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.96329416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16652672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81624.6811128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.288153964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.71515172
X-RAY DIFFRACTIONr_chiral_restr0.0860.23292
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.210062
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.214830
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2653
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4963.513617
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.874421464
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.62158964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0686.57952
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

Ens-ID: 1 / Number: 5363 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.130.5
2Bmedium positional0.140.5
3Cmedium positional0.140.5
4Dmedium positional0.130.5
1Amedium thermal0.132
2Bmedium thermal0.142
3Cmedium thermal0.132
4Dmedium thermal0.142
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.396 381
Rwork0.342 6711
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)
10.0156-0.10020.171.2014-0.87271.93490.12470.05660.0806-0.2254-0.1399-0.0439-0.0425-0.06350.0151-0.04710.0879-0.0353-0.08490.0957-0.069554.604120.29349.6447
20.00780.0565-0.12141.1694-0.8671.88840.1151-0.0574-0.06310.1971-0.1407-0.04530.0731-0.04740.0256-0.0438-0.07260.0262-0.07390.0853-0.09654.4163-21.2635-9.6555
31.9083-0.88150.18641.1864-0.07050.01850.0189-0.0631-0.0351-0.0515-0.1423-0.22990.07390.0570.1234-0.08520.0925-0.0293-0.0770.1037-0.030797.8168-21.265752.6642
41.8003-0.8102-0.12481.13970.0980.01090.0173-0.04770.0695-0.0576-0.12820.1947-0.0464-0.05240.1109-0.0890.08320.0329-0.0616-0.0617-0.0523117.09320.287252.7548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 695
2X-RAY DIFFRACTION2B3 - 695
3X-RAY DIFFRACTION3C3 - 695
4X-RAY DIFFRACTION4D3 - 695

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