[English] 日本語
Yorodumi
- PDB-3lqk: Crystal structure of dipicolinate synthase subunit B from Bacillu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lqk
TitleCrystal structure of dipicolinate synthase subunit B from Bacillus halodurans C
ComponentsDipicolinate synthase subunit B
KeywordsOXIDOREDUCTASE / dipicolinate synthase / Flavoprotein / PSI2 / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


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 halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNocek, B. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of dipicolinate synthase subunit B from Bacillus halodurans C
Authors: Nocek, B. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionFeb 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dipicolinate synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5863
Polymers22,3961
Non-polymers1902
Water1,51384
1
A: Dipicolinate synthase subunit B
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)135,51718
Polymers134,3776
Non-polymers1,14012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area16820 Å2
ΔGint-164 kcal/mol
Surface area42920 Å2
MethodPISA
2
A: Dipicolinate synthase subunit B
hetero molecules

A: Dipicolinate synthase subunit B
hetero molecules

A: Dipicolinate synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7589
Polymers67,1893
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5070 Å2
ΔGint-59 kcal/mol
Surface area24800 Å2
MethodPISA
3
A: Dipicolinate synthase subunit B
hetero molecules

A: Dipicolinate synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1726
Polymers44,7922
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Buried area2460 Å2
ΔGint-36 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.185, 110.185, 71.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-272-

HOH

-
Components

#1: Protein Dipicolinate synthase subunit B


Mass: 22396.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: spoVFB, BH2402 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: Q9KA88
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.3 M 195NSBD, 2.0 M Ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 15060 / Num. obs: 14994 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.8 / Num. unique all: 742 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
DMmodel building
SHELXmodel building
MLPHAREphasing
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.987 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.16 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21296 749 5 %RANDOM
Rwork0.16658 ---
all0.17 14930 --
obs0.16882 14181 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.038 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 10 84 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221511
X-RAY DIFFRACTIONr_bond_other_d0.0020.02997
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9752058
X-RAY DIFFRACTIONr_angle_other_deg1.07732471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54925.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.912155
X-RAY DIFFRACTIONr_chiral_restr0.1230.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0941.5979
X-RAY DIFFRACTIONr_mcbond_other0.3011.5392
X-RAY DIFFRACTIONr_mcangle_it2.02121589
X-RAY DIFFRACTIONr_scbond_it3.2453532
X-RAY DIFFRACTIONr_scangle_it5.5414.5467
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 60 -
Rwork0.194 1029 -
obs--99 %
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)
11.2519-0.1598-0.54692.0684-0.05810.8456-0.03270.2485-0.1127-0.02750.0721-0.1268-0.011-0.0182-0.03940.15660.0038-0.00380.142-0.04160.13139.627841.8054-1.7784
23.8884-4.45110.60827.0889-1.96423.1194-0.01940.24820.1196-0.0497-0.0165-0.4956-0.09540.07730.03590.130.01390.03580.15490.00360.144617.488941.8877-2.9022
32.1807-1.11930.67464.4914-1.42860.53060.03830.2607-0.1278-0.0201-0.15090.05150.0142-0.00780.11260.14210.02470.00430.1821-0.0440.1117.416641.0005-5.2427
41.6418-5.44535.70212.4602-9.39218.7490.08910.1064-0.0068-0.4398-0.0151-0.00110.3940.0252-0.0740.4453-0.00890.01590.3230.01360.073610.050850.5485-19.4317
56.8588-3.42150.22574.2477-1.02460.6576-0.02330.4561-0.1093-0.2452-0.0280.05130.03480.0170.05130.14770.0137-0.00850.1951-0.04350.05364.960443.3046-11.0376
60.54360.445-0.181.33980.4620.35090.01250.0911-0.0279-0.0109-0.05860.0139-0.0135-0.07240.04610.14610.00830.01140.1668-0.00870.12911.243548.33111.5423
70.49240.20720.19510.26790.24960.31970.00350.02280.0516-0.0159-0.060.038-0.0245-0.03160.05650.15930.00890.00990.15120.00080.13054.038852.41175.9535
80.61650.7954-0.3863.02880.48791.4062-0.0564-0.0230.07790.05990.0765-0.08110.0786-0.0224-0.02010.14550.00520.01570.15080.00350.13223.220650.487114.7941
91.65221.06890.37361.83090.25580.16160.0233-0.0053-0.09930.0533-0.0532-0.09190.02470.09340.02990.14230.01010.01280.15580.00920.121816.316347.529810.0956
10-1.1217-0.32881.03692.4137-5.09979.37070.0282-0.0719-0.05390.0528-0.5352-0.3441-0.00580.76230.5070.13060.01190.0160.20520.0530.230818.695145.629614.9753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 28
3X-RAY DIFFRACTION3A29 - 43
4X-RAY DIFFRACTION4A44 - 59
5X-RAY DIFFRACTION5A60 - 75
6X-RAY DIFFRACTION6A76 - 104
7X-RAY DIFFRACTION7A105 - 141
8X-RAY DIFFRACTION8A142 - 150
9X-RAY DIFFRACTION9A151 - 185
10X-RAY DIFFRACTION10A186 - 195

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more