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- PDB-2hkv: CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1... -

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Basic information

Entry
Database: PDB / ID: 2hkv
TitleCRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1237) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.70 A RESOLUTION
ComponentsHypothetical protein
KeywordsDNA BINDING PROTEIN / PUTATIVE MEMBER OF THE DINB FAMILY / 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 / Uncharacterized protein / :
Similarity search - Component
Biological speciesExiguobacterium sibiricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of conserved hypothetical protein RBL00553 (ZP_00537729.1) from EXIGUOBACTERIUM SP. 255-15 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 14, 2016Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jan 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.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.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_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: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5365
Polymers17,3711
Non-polymers1654
Water1,17165
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,07210
Polymers34,7422
Non-polymers3308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3860 Å2
ΔGint-100 kcal/mol
Surface area13140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.020, 45.020, 131.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Hypothetical protein


Mass: 17371.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Strain: 255-15 / Gene: ZP_00537729.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q41IB9, UniProt: B1YEV7*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2142.07
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2771vapor diffusion, sitting drop, nanodrop20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2932vapor diffusion, sitting drop, nanodrop20.0% PEG-3350, 0.2M MgSO4,, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97925
SYNCHROTRONSSRL BL9-220.92522, 0.97934
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJun 17, 2006Flat collimating mirror, toroid focusing mirror
MARMOSAIC 325 mm CCD2CCDJun 17, 2006Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.925221
30.979341
ReflectionResolution: 1.7→25.094 Å / Num. obs: 17704 / % possible obs: 99.8 % / Redundancy: 9.38 % / Biso Wilson estimate: 37.034 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.58
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.7-1.767.010.971.9910939153399.8
1.76-1.830.7322.811534160092.5
1.83-1.910.5713.411264156593.5
1.91-2.020.3755.213211184997
2.02-2.140.262711687164398.6
2.14-2.310.22610.118428178199.4
2.31-2.540.18712.921841174899.8
2.54-2.90.15214.621615175299.9
2.9-25.10.11517220911825100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→25.094 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.318 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.111
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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE ASSIGNMENT OF THE METAL AS PREDOMINATELY NICKEL IS BASED ON BOTH X-RAY FLUORECENCE METAL SCAN AND DIFFERENCE MAPS (ABOVE AND BELOW NICKEL AND ZINC EDGES). 5. THE ASSIGNMENT OF CHLORIDES ARE BASED ON DIFFERENCE DENSITY. 6. THE DISORDER ON TWO-FOLD BY RESIDUE 4 INDICATED THAT THE SPACE GROUP IS NOT STRICTLY P3221 BUT P32, REFINEMENT IN P3221 RESULTS ONLY ~1% INCREASE IN RFACTOR AND RFREE COMPARED TO P32, THUS THE SPACE GROUP WAS ASSIGNED AS HIGHER SYMMETRY P3221. 7. THE EXPERIMENTAL PHASES ARE FROM A DIFFERENT CRYSTAL, THEY ARE USED AS RESTRAINTS IN REFINEMENT. 8. DENSITY FOR RESIDUE 99 IS POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1361 7.7 %RANDOM
Rwork0.181 ---
all0.185 ---
obs0.18514 17699 99.86 %-
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: 33.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.32 Å20 Å2
2---0.63 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 4 65 1266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221245
X-RAY DIFFRACTIONr_bond_other_d0.0010.02810
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9351704
X-RAY DIFFRACTIONr_angle_other_deg1.02531960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2735151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.46523.11561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21915199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0441510
X-RAY DIFFRACTIONr_chiral_restr0.10.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
X-RAY DIFFRACTIONr_nbd_refined0.2230.2305
X-RAY DIFFRACTIONr_nbd_other0.1790.2812
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2615
X-RAY DIFFRACTIONr_nbtor_other0.0910.2587
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.242
X-RAY DIFFRACTIONr_metal_ion_refined0.4010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.24
X-RAY DIFFRACTIONr_mcbond_it2.6423815
X-RAY DIFFRACTIONr_mcbond_other0.6073301
X-RAY DIFFRACTIONr_mcangle_it3.50751197
X-RAY DIFFRACTIONr_scbond_it5.7068581
X-RAY DIFFRACTIONr_scangle_it7.6411505
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 99 -
Rwork0.269 1168 -
obs-1267 99.69 %
Refinement TLS params.Method: refined / Origin x: 7.135 Å / Origin y: -0.881 Å / Origin z: -8.439 Å
111213212223313233
T-0.0121 Å2-0.0881 Å2-0.0672 Å2--0.013 Å2-0.0843 Å2---0.0639 Å2
L2.6534 °2-0.7319 °21.4145 °2-2.6711 °2-0.8647 °2--2.0371 °2
S0.2271 Å °0.5931 Å °-0.5004 Å °-0.2802 Å °-0.0447 Å °0.112 Å °-0.0122 Å °0.4846 Å °-0.1824 Å °
Refinement TLS groupSelection: ALL

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