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- PDB-3mcu: Crystal structure of the dipicolinate synthase chain B from Bacil... -

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Basic information

Entry
Database: PDB / ID: 3mcu
TitleCrystal structure of the dipicolinate synthase chain B from Bacillus cereus. Northeast Structural Genomics Consortium Target BcR215.
ComponentsDipicolinate synthase, B chain
KeywordsOXIDOREDUCTASE / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / sporulation resulting in formation of a cellular spore / oxidoreductase activity
Similarity search - Function
Dipicolinic acid synthetase, subunit B / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dipicolinate synthase subunit B
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsVorobiev, S. / Lew, S. / Abashidze, M. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. ...Vorobiev, S. / Lew, S. / Abashidze, M. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the dipicolinate synthase chain B from Bacillus cereus.
Authors: Vorobiev, S. / Lew, S. / Abashidze, M. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Foote, E.L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipicolinate synthase, B chain
B: Dipicolinate synthase, B chain
C: Dipicolinate synthase, B chain
D: Dipicolinate synthase, B chain
E: Dipicolinate synthase, B chain
F: Dipicolinate synthase, B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,56313
Polymers139,8986
Non-polymers6657
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16080 Å2
ΔGint-119 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.082, 129.257, 132.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHexamer according to aggregation screening

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Components

#1: Protein
Dipicolinate synthase, B chain


Mass: 23316.361 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579/DSM 31 / Gene: BC_3800 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q819Z6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 14% PEG 20000, 0.06M potassium phosphate, 0.1M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 112783 / Num. obs: 106354 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.95 / Num. unique all: 11290 / % possible all: 89.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LQK

3lqk


Resolution: 2.303→38.253 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 5341 5.08 %RANDOM
Rwork0.1964 ---
obs0.1987 105071 93.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.203 Å2 / ksol: 0.337 e/Å3
Refinement stepCycle: LAST / Resolution: 2.303→38.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8489 0 35 425 8949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088673
X-RAY DIFFRACTIONf_angle_d1.11411724
X-RAY DIFFRACTIONf_dihedral_angle_d17.2643256
X-RAY DIFFRACTIONf_chiral_restr0.0731360
X-RAY DIFFRACTIONf_plane_restr0.0051491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3027-2.32880.31721440.26642363X-RAY DIFFRACTION66
2.3288-2.35620.21341620.19913237X-RAY DIFFRACTION89
2.3562-2.38490.22641790.19293278X-RAY DIFFRACTION92
2.3849-2.41510.25942020.20133312X-RAY DIFFRACTION94
2.4151-2.44690.26991910.20973437X-RAY DIFFRACTION97
2.4469-2.48040.26841760.20853544X-RAY DIFFRACTION98
2.4804-2.51580.26751640.20853518X-RAY DIFFRACTION99
2.5158-2.55340.26581890.20333589X-RAY DIFFRACTION100
2.5534-2.59330.23121970.19423610X-RAY DIFFRACTION100
2.5933-2.63580.31331940.18843544X-RAY DIFFRACTION100
2.6358-2.68120.28291890.19293547X-RAY DIFFRACTION100
2.6812-2.730.2212050.193541X-RAY DIFFRACTION100
2.73-2.78250.25341890.19633600X-RAY DIFFRACTION100
2.7825-2.83920.27071940.20363585X-RAY DIFFRACTION100
2.8392-2.9010.29572030.2073560X-RAY DIFFRACTION100
2.901-2.96840.25951700.19893569X-RAY DIFFRACTION100
2.9684-3.04260.25722040.18773550X-RAY DIFFRACTION100
3.0426-3.12480.19261600.18753616X-RAY DIFFRACTION100
3.1248-3.21680.24971930.18083561X-RAY DIFFRACTION100
3.2168-3.32050.21611930.19623544X-RAY DIFFRACTION100
3.3205-3.43910.28482330.19763468X-RAY DIFFRACTION99
3.4391-3.57670.20191300.19812806X-RAY DIFFRACTION83
3.5767-3.73940.163660.2295116X-RAY DIFFRACTION7
3.7394-3.93630.22292120.17813235X-RAY DIFFRACTION92
3.9363-4.18270.21991610.17343472X-RAY DIFFRACTION96
4.1827-4.50520.22211870.16593574X-RAY DIFFRACTION100
4.5052-4.95770.20771500.17173580X-RAY DIFFRACTION100
4.9577-5.67310.23982040.19983552X-RAY DIFFRACTION100
5.6731-7.13990.21631900.20243500X-RAY DIFFRACTION98
7.1399-38.25810.19671700.20513322X-RAY DIFFRACTION93
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.45740.36840.69090.77810.53161.7322-0.0256-0.04110.0376-0.0227-0.0360.0722-0.2313-0.1355-00.16350.0495-0.01020.1314-0.00070.143415.0434-16.390324.7573
20.4008-0.43380.27781.1797-0.13671.285-0.02990.00190.07080.0627-0.0368-0.2352-0.19070.080500.2116-0.0697-0.04590.14510.00070.225
30.382-0.64770.30171.3487-0.30111.066-0.0487-0.0527-0.06540.12450.08990.0877-0.0579-0.2357-00.14510.04470.04320.25060.01340.1665
40.8037-0.8132-0.65091.37790.37111.16070.0007-0.09970.04750.1742-0.0082-0.11540.01090.1315-00.0978-0.0064-0.02390.13090.01620.1202
50.39160.67530.13111.2721-0.21141.3156-0.01960.0475-0.0741-0.0889-0.0021-0.17030.12420.148900.11010.03130.05630.17760.00350.189
60.98270.1175-1.03281.2872-0.19891.45-0.0110.1323-0.0679-0.1963-0.05190.12670.0894-0.215100.1143-0.0311-0.04870.1781-0.02840.161
Refinement TLS groupSelection details: chain F

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