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- PDB-2aj7: Crystal structure of a putative contractile protein (bh3618) from... -

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Basic information

Entry
Database: PDB / ID: 2aj7
TitleCrystal structure of a putative contractile protein (bh3618) from bacillus halodurans at 1.67 A resolution
Componentshypothetical protein BH3618
KeywordsCONTRACTILE PROTEIN / Bh3618-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


bacterial-type flagellum assembly / regulation of translation / cytoplasm
Similarity search - Function
BH3618-like / BH3618-like / Flagellar assembly factor FliW / Flagellar assembly factor FliW domain superfamily / FliW protein / Roll / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / : / NICKEL (II) ION / Flagellar assembly factor FliW
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.67 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (10176242) from Bacillus halodurans at 1.67 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_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.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN THE DATABASE. SEQUENCING CONFIRMED ...SEQUENCE THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN THE DATABASE. SEQUENCING CONFIRMED THE ENGINEERED MUTATIONS E41A AND E42A AS WELL AS THE N9S, V81A AND D134N STRAIN VARIATIONS THE ELECTRON DENSITY SUPPORTS THIS ASSIGNMENT. NOTE THAT THE ENVIRONMENT AROUND ALA-41 WITHIN THE STRUCTURE SUGGESTS THAT A GLUTAMATE SIDE CHAIN AT THIS POSITION IS UNLIKELY WITHOUT STRUCTURAL CHANGES. THUS, THIS E41A MUTATION MIGHT HAVE INDUCED LOCAL CONFORMATION CHANGES AROUND RESIDUE 41.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein BH3618
B: hypothetical protein BH3618
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,38323
Polymers37,2182
Non-polymers1,16521
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint10 kcal/mol
Surface area16390 Å2
MethodPISA
2
A: hypothetical protein BH3618
B: hypothetical protein BH3618
hetero molecules

A: hypothetical protein BH3618
B: hypothetical protein BH3618
hetero molecules

A: hypothetical protein BH3618
B: hypothetical protein BH3618
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,14869
Polymers111,6536
Non-polymers3,49463
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area22460 Å2
ΔGint0 kcal/mol
Surface area42900 Å2
MethodPISA
3
A: hypothetical protein BH3618
B: hypothetical protein BH3618
hetero molecules

A: hypothetical protein BH3618
B: hypothetical protein BH3618
hetero molecules

A: hypothetical protein BH3618
B: hypothetical protein BH3618
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,14869
Polymers111,6536
Non-polymers3,49463
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area18610 Å2
ΔGint7 kcal/mol
Surface area45960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.810, 108.810, 82.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-152-

NI

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEVALVALAA1 - 12713 - 139
21MSEMSEVALVALBB1 - 12713 - 139
32ALAALALEULEUAA132 - 139144 - 151
42ALAALALEULEUBB132 - 139144 - 151

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein hypothetical protein BH3618


Mass: 18608.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: A-59 / Gene: 10176242 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K6V7

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Non-polymers , 5 types, 422 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.7763.11
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop7.30.2M KFormate, 20.9% PEG-3350, No Buffer, pH 7.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2732vapor diffusion, sitting drop, nanodrop7.10.2M NaF, 20.0% PEG-3350, No Buffer, pH 7.1, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.000001
SYNCHROTRONSSRL BL9-220.91162, 0.97913, 0.97929
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJul 18, 2005flat mirror
MARMOSAIC 325 mm CCD2CCDJul 3, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1BENT SI-111 MONOCHROMATOR HORRIZONTLALLY FOCUSINGSINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL MONOCHROMATORMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0000011
20.911621
30.979131
40.979291
ReflectionResolution: 1.67→47.14 Å / Num. obs: 64155 / % possible obs: 93.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.93
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.67-1.7381.40.7531.72264671037681.4
1.73-1.8850.6122.152760910796
1.8-1.8888.30.4252.972787810908
1.88-1.9891.70.3074.082990111709
1.98-2.195.20.1936.222993511714
2.1-2.2796.60.12793268012778
2.27-2.4997.90.13713.135608211907
2.49-2.8598.90.10716.256391012572
2.85-3.5999.30.0625.566394912614
3.5999.60.03842.096416212693

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata processing
PDB_EXTRACT1.601data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.67→47.12 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.537 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. AN METAL OF UNKNOWN TYPE IS LOCATED ON THE 3-FOLD CRYSTALLOGRAPHIC AXIS, IT IS COORDINATED BY HIS0, HIS-2 OF CHAIN B AND THEIR ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. AN METAL OF UNKNOWN TYPE IS LOCATED ON THE 3-FOLD CRYSTALLOGRAPHIC AXIS, IT IS COORDINATED BY HIS0, HIS-2 OF CHAIN B AND THEIR SYMMETRIC MATES. THE IDENTITY OF THE METAL IS TENTATIVELY ASSIGNED AS A NICKLE (NI).
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3213 5 %RANDOM
Rwork0.167 ---
all0.169 ---
obs-60915 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.674 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0.73 Å20 Å2
2---1.45 Å20 Å2
3---2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.67→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 71 401 2884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222638
X-RAY DIFFRACTIONr_bond_other_d0.0020.022475
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9723583
X-RAY DIFFRACTIONr_angle_other_deg0.80835783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21925.398113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82915451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.796155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_nbd_refined0.2160.2457
X-RAY DIFFRACTIONr_nbd_other0.1850.22561
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21283
X-RAY DIFFRACTIONr_nbtor_other0.0840.21558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2303
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.225
X-RAY DIFFRACTIONr_mcbond_it2.50251606
X-RAY DIFFRACTIONr_mcbond_other1.195634
X-RAY DIFFRACTIONr_mcangle_it3.59262624
X-RAY DIFFRACTIONr_scbond_it3.91861042
X-RAY DIFFRACTIONr_scangle_it5.5457.5939
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2015 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.330.5
MEDIUM THERMAL1.132
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 239 -
Rwork0.271 4524 -
obs--100 %
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)
11.81970.04050.3861.9921.05791.48320.0749-0.04180.1813-0.2091-0.0742-0.0616-0.2215-0.1169-0.0007-0.00440.06170.05650.02530.0348-0.091826.6758.81564.995
22.3822-0.54020.2941.35030.47221.11620.05180.0328-0.15560.0113-0.0240.13880.0005-0.1205-0.0278-0.0460.03010.00490.00070.0434-0.09630.150435.425152.4685
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-8 - 1484 - 160
22BB-2 - 14610 - 158

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