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- PDB-2f22: CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTE... -

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Basic information

Entry
Database: PDB / ID: 2f22
TitleCRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTEIN (BH3987) FROM BACILLUS HALODURANS AT 1.42 A RESOLUTION
ComponentsBH3987
KeywordsMETAL BINDING PROTEIN / PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


DNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Unknown
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of BH3987 from Bacillus halodurans at 1.42 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 30, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH3987
B: BH3987
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0135
Polymers33,8732
Non-polymers1403
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-51 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.358, 77.705, 80.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BH3987


Mass: 16936.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10176612 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RC77
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 277 K / pH: 6.6
Details: 0.2M (NH4)2 Tartrate, 20.0% PEG-3350, No Buffer, pH 6.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796, 0.9797
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97971
ReflectionResolution: 1.35→24.3 Å / Num. obs: 58327 / % possible obs: 98.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.42-1.4691.82.90.4841.539410.484
1.46-1.595.83.20.3851.940470.385
1.5-1.5498.13.50.3262.139630.326
1.54-1.591003.60.2872.539930.287
1.59-1.641003.60.248338390.248
1.64-1.71003.60.2133.437490.213
1.7-1.761003.60.1913.835860.191
1.76-1.831003.60.164.434850.16
1.83-1.911003.60.139533320.139
1.91-2.011003.60.125.532030.12
2.01-2.121006.70.138530330.138
2.12-2.251007.20.1225.629150.122
2.25-2.499.97.30.1086.426930.108
2.4-2.591007.20.0937.425640.093
2.59-2.841007.20.0838.323330.083
2.84-3.1899.97.10.0758.721400.075
3.18-3.6799.87.10.0669.818910.066
3.67-4.4999.66.90.05910.716330.059
4.49-6.3599.46.70.0659.612660.065
6.35-24.396.25.90.0698.67210.069

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.42→23.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.778 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. NI ATOMS MODELED BASED ON ANOMALOUS AND DIFFERENCE MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2955 5.1 %RANDOM
Rwork0.157 ---
all0.158 ---
obs-55316 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.42→23.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 3 412 2720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222520
X-RAY DIFFRACTIONr_bond_other_d0.0010.021754
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9633433
X-RAY DIFFRACTIONr_angle_other_deg1.13534324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5775329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81224.545121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23515499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6591515
X-RAY DIFFRACTIONr_chiral_restr0.1050.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022799
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02498
X-RAY DIFFRACTIONr_nbd_refined0.2340.2553
X-RAY DIFFRACTIONr_nbd_other0.190.21802
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21209
X-RAY DIFFRACTIONr_nbtor_other0.0880.21219
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2302
X-RAY DIFFRACTIONr_metal_ion_refined0.310.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0450.21
X-RAY DIFFRACTIONr_mcbond_it1.22331496
X-RAY DIFFRACTIONr_mcbond_other0.3513610
X-RAY DIFFRACTIONr_mcangle_it2.12752439
X-RAY DIFFRACTIONr_scbond_it3.83281062
X-RAY DIFFRACTIONr_scangle_it5.33911969
LS refinement shellResolution: 1.419→1.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 190 -
Rwork0.261 3678 -
obs--89.87 %
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)
10.5585-0.2065-0.15441.490.45390.72450.0071-0.01320.0067-0.0052-0.01160.0028-0.0054-0.00350.00450.0095-0.00730.00980.0176-0.00120.01118.61064.196420.2861
20.7147-0.23960.13082.23820.70732.65590.05240.01980.01160.02530.0198-0.03070.09090.0462-0.07220.0016-0.0090.0030.0245-0.00790.035815.9203-4.034214.882
30.93560.6390.50712.52691.58342.8390.01340.00190.01150.0153-0.06340.082-0.0246-0.08860.05-0.0073-0.00080.00930.02330.00230.013721.90948.924618.763
40.66790.0051-0.24671.66730.98581.3661-0.0073-0.00430.0260.00740.0026-0.06760.0209-0.01670.00480.01760.00970.00390.02510.00980.031636.721313.729615.9002
52.54351.2602-0.15194.0584-0.27531.89350.00190.0436-0.114-0.08770.0035-0.1411-0.0367-0.0417-0.00550.04510.00880.03570.0738-0.01420.051441.31534.20397.6074
60.5179-0.3471-0.19965.94911.46920.96850.0310.0143-0.010.0189-0.016-0.1355-0.0147-0.0215-0.015-0.0004-0.00240.01070.02530.00380.015931.186813.283217.3402
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 431 - 44
22AA44 - 10045 - 101
33AA101 - 141102 - 142
44BB1 - 482 - 49
55BB49 - 10050 - 101
66BB101 - 143102 - 144

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