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- PDB-3tvz: Structure of Bacillus subtilis HmoB -

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Basic information

Entry
Database: PDB / ID: 3tvz
TitleStructure of Bacillus subtilis HmoB
ComponentsPutative uncharacterized protein yhgC
KeywordsOXIDOREDUCTASE / putative monooxygenase / ABM family / ferredoxin fold / monooxygenase
Function / homology
Function and homology information


: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ABM domain-containing protein
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsChoe, J. / Choi, S. / Park, S.
CitationJournal: Bmb Rep / Year: 2012
Title: Bacillus subtilis HmoB is a heme oxygenase with a novel structure.
Authors: Park, S. / Choi, S. / Choe, J.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein yhgC
B: Putative uncharacterized protein yhgC
C: Putative uncharacterized protein yhgC


Theoretical massNumber of molelcules
Total (without water)58,5313
Polymers58,5313
Non-polymers00
Water5,423301
1
A: Putative uncharacterized protein yhgC


Theoretical massNumber of molelcules
Total (without water)19,5101
Polymers19,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein yhgC


Theoretical massNumber of molelcules
Total (without water)19,5101
Polymers19,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein yhgC


Theoretical massNumber of molelcules
Total (without water)19,5101
Polymers19,5101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.799, 64.799, 392.591
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative uncharacterized protein yhgC


Mass: 19510.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria)
Strain: ATCC 23059 / NRRL B-14472 / W23 / Gene: yhgC, BSUW23_05110 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E0TXX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 8.5
Details: 28% PEG 4000, 0.2M Magnesium chloride, 0.1M Tris-Hcl pH8.5, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.97865
SYNCHROTRONSPring-8 BL41XU20.97904
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDJun 14, 2010
ADSC QUANTUM 2102CCDMay 31, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978651
20.979041
ReflectionResolution: 2→50 Å / Num. all: 34657 / Num. obs: 34657 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→48.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.525 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1736 5 %RANDOM
Rwork0.1959 ---
obs0.1986 34446 99.84 %-
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 max: 196.55 Å2 / Biso mean: 42.15 Å2 / Biso min: 24.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 0 301 3735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223515
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.944771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1565419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60324.716176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84815588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.681516
X-RAY DIFFRACTIONr_chiral_restr0.1340.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022679
X-RAY DIFFRACTIONr_nbd_refined0.2320.21776
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2309
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.212
X-RAY DIFFRACTIONr_mcbond_it1.0311.52186
X-RAY DIFFRACTIONr_mcangle_it1.65623439
X-RAY DIFFRACTIONr_scbond_it2.66431526
X-RAY DIFFRACTIONr_scangle_it4.0654.51332
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 131 -
Rwork0.172 2318 -
all-2449 -
obs--99.84 %
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)
12.8278-1.79440.74853.0404-0.39421.8609-0.15150.04250.3687-0.09660.0991-0.0984-0.21040.00740.0524-0.0044-0.0255-0.0124-0.11430.0401-0.30439.83646.031183.795
23.47220.5476-0.17893.7674-0.11112.1295-0.14020.3869-0.4789-0.39220.01770.13960.3458-0.22840.12250.0286-0.07590.0278-0.0336-0.0921-0.294.35212.285183.597
31.65790.3621-0.7361.62620.51322.71410.0244-0.08980.0620.06830.028-0.1332-0.09360.2826-0.0524-0.0578-0.0055-0.0038-0.0379-0.0049-0.326536.02924.733178.408
40.6338-0.3426-0.22580.43230.20660.8656-0.00980.08340.0359-0.0629-0.0107-0.0013-0.0044-0.02670.0205-0.018-0.0202-0.0104-0.04920.0033-0.299820.7928.392181.775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 172
2X-RAY DIFFRACTION2B7 - 172
3X-RAY DIFFRACTION3C7 - 172
4X-RAY DIFFRACTION4C173 - 403

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