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- PDB-2qe9: Crystal structure of a putative metal-dependent hydrolase (yiza, ... -

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Basic information

Entry
Database: PDB / ID: 2qe9
TitleCrystal structure of a putative metal-dependent hydrolase (yiza, bsu10800) from bacillus subtilis at 1.90 A resolution
ComponentsUncharacterized protein yizA
KeywordsHYDROLASE / Dinb/yfit-like putative metalloenzymes fold / 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
CITRIC ACID / NICKEL (II) ION / Uncharacterized protein YizA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein BSU10800 (YP_054576.1) from Bacillus subtilis at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.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 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein yizA
B: Uncharacterized protein yizA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1437
Polymers42,5792
Non-polymers5645
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-56 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.184, 53.184, 251.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein yizA


Mass: 21289.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: YP_054576.1, yizA, yucC, BSU10800 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7WY73
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: NANODROP, 0.2M NaCl, 10.0% PEG 3000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979251
ReflectionResolution: 1.9→29.761 Å / Num. obs: 29798 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.956.90.920.81466221290.92100
1.95-26.80.7221.11415920720.722100
2-2.066.80.5391.31392020530.539100
2.06-2.126.80.411.81350519950.41100
2.12-2.196.90.3262.31308019050.326100
2.19-2.276.80.2652.81272618730.265100
2.27-2.366.80.2313.31214517990.231100
2.36-2.456.80.18841185517410.188100
2.45-2.566.70.1634.61136816880.163100
2.56-2.696.70.1325.51078516120.132100
2.69-2.836.70.1176.11032615330.117100
2.83-36.70.0967.4976014620.096100
3-3.216.60.0887.6913113740.088100
3.21-3.476.60.0837.7851812980.083100
3.47-3.86.40.0698.2783812160.069100
3.8-4.256.50.05810.3706910860.058100
4.25-4.916.30.05310.862689880.053100
4.91-6.016.30.0511.853498550.05100
6.01-8.560.0481241326930.048100
8.5-29.7615.10.04612.421834260.04697.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.761 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.23 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.143
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 94-99 IN CHAIN A AND 152-159 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. NI ION IS MODELED BASED ON METAL EXCITATION SCAN. 5. CITRATE ION AND ETHYLENE GLYCOL FROM THE CRYSTALLIZATION/CRYO SOLUTIONS ARE MODELED. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 7. RAMACHANDRAN OUTLIER RESIDUE -7 IN CHAIN A LIES IN A DISORDERED REGION. 8. 36 UNUSUALLY STRONG REFLECTIONS WERE OMITTED FROM THE FINAL REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1500 5.1 %RANDOM
Rwork0.185 ---
obs0.187 29655 99.83 %-
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: 27.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2---1.3 Å20 Å2
3---2.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 32 235 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212853
X-RAY DIFFRACTIONr_bond_other_d0.0040.021855
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9083886
X-RAY DIFFRACTIONr_angle_other_deg1.3134495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6045332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14923.514148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90415465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2241515
X-RAY DIFFRACTIONr_chiral_restr0.0750.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023158
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02625
X-RAY DIFFRACTIONr_nbd_refined0.1880.2630
X-RAY DIFFRACTIONr_nbd_other0.1390.21860
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21377
X-RAY DIFFRACTIONr_nbtor_other0.0720.21322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1180.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.213
X-RAY DIFFRACTIONr_mcbond_it1.73331724
X-RAY DIFFRACTIONr_mcbond_other0.4243665
X-RAY DIFFRACTIONr_mcangle_it2.60852658
X-RAY DIFFRACTIONr_scbond_it4.40281361
X-RAY DIFFRACTIONr_scangle_it5.67111224
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 103 -
Rwork0.232 2019 -
obs-2122 99.86 %
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)
11.9003-0.8740.09722.6665-0.3991.87460.13460.34490.016-0.2775-0.2076-0.17690.08330.18110.073-0.14180.06110.0159-0.0883-0.0025-0.276-10.63817.65111.831
22.01690.56820.71842.11540.48271.77090.09340.02340.05250.0816-0.08290.3351-0.0101-0.2533-0.0105-0.16040.02160.0228-0.141-0.025-0.163-29.08924.31422.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-11 - 938 - 112
2X-RAY DIFFRACTION1AA100 - 159119 - 178
3X-RAY DIFFRACTION2BB-10 - 1519 - 170

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