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- PDB-1rxq: YfiT from Bacillus subtilis is a probable metal-dependent hydrola... -

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Basic information

Entry
Database: PDB / ID: 1rxq
TitleYfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology
ComponentsyfiT
KeywordsMETAL BINDING PROTEIN / Nickel-binding / hydrolase / helix-bundle / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / metal-binding protein
Function / homology
Function and homology information


Hydrolases / hydrolase activity / zinc ion binding / cytoplasm
Similarity search - Function
Putative metal-dependent hydrolase YfiT / DinB-like domain / DinB superfamily / 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
ALANINE / GLUTAMIC ACID / GLYCINE / NICKEL (II) ION / SERINE / THREONINE / : / Putative metal-dependent hydrolase YfiT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsRajan, S.S. / Yang, X. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Biochemistry / Year: 2004
Title: YfiT from Bacillus subtilis Is a Probable Metal-Dependent Hydrolase with an Unusual Four-Helix Bundle Topology
Authors: Rajan, S.S. / Yang, X. / Shuvalova, L. / Collart, F. / Anderson, W.F.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_keywords / struct_ncs_dom_lim / 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.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_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: yfiT
B: yfiT
C: yfiT
D: yfiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,41914
Polymers83,5444
Non-polymers87510
Water8,449469
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: yfiT
D: yfiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,53010
Polymers41,7722
Non-polymers7588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-28 kcal/mol
Surface area16110 Å2
MethodPISA, PQS
3
B: yfiT
C: yfiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8894
Polymers41,7722
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-40 kcal/mol
Surface area15920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.370, 50.420, 89.410
Angle α, β, γ (deg.)104.38, 90.61, 112.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 10 - 178 / Label seq-ID: 10 - 178

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21DD
12BB
22CC

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
yfiT


Mass: 20885.986 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yfiT / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: GenBank: 16077906, UniProt: O31562*PLUS

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Non-polymers , 7 types, 479 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 75437 / Num. obs: 70594 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.072 / Net I/σ(I): 6.4
Reflection shellResolution: 1.7→1.744 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.21 / % possible all: 67.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.36 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21708 3743 5 %RANDOM
Rwork0.18644 ---
obs0.18798 70594 93.58 %-
all-74337 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.27 Å20.09 Å2
2--0.18 Å20.12 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 41 469 6200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215851
X-RAY DIFFRACTIONr_bond_other_d0.0010.025188
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.9327936
X-RAY DIFFRACTIONr_angle_other_deg0.667312107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5895689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026390
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021186
X-RAY DIFFRACTIONr_nbd_refined0.2110.31359
X-RAY DIFFRACTIONr_nbd_other0.2390.35959
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.53398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5517
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.381
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.2251.53460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.33425607
X-RAY DIFFRACTIONr_scbond_it4.98932391
X-RAY DIFFRACTIONr_scangle_it6.9094.52329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2657tight positional0.270.05
2B2658tight positional0.260.05
1A2657tight thermal0.890.5
2B2658tight thermal0.940.5
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 204
Rwork0.239 3603
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)
12.2027-1.2457-0.38442.54440.58851.8721-0.0361-0.22350.17490.3440.0759-0.12060.01710.2144-0.03970.1174-0.0403-0.01660.1362-0.00330.053814.5981-4.4341-9.5267
21.4933-0.6035-0.22022.56710.57952.13650.1110.1190.2218-0.2343-0.0377-0.2472-0.04130.1593-0.07320.07650.00310.04140.10240.02880.1134-12.5035-6.572917.7317
32.4063-1.1913-0.19133.1564-0.34171.6975-0.00060.0621-0.1491-0.05410.05230.12420.2435-0.139-0.05170.0652-0.0408-0.02480.042-0.0060.0378-24.7252-20.325432.644
40.9632-1.21790.04864.1095-0.11220.83040.0950.1441-0.1177-0.3077-0.11720.11090.07180.06550.02220.07930.0055-0.0190.0929-0.00790.06685.5765-10.0298-30.7795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 17810 - 178
2X-RAY DIFFRACTION2BB10 - 17810 - 178
3X-RAY DIFFRACTION3CC10 - 17810 - 178
4X-RAY DIFFRACTION4DD10 - 17810 - 178

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