[English] 日本語
Yorodumi
- PDB-5bp8: ent-Copalyl diphosphate synthase from Streptomyces platensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bp8
Titleent-Copalyl diphosphate synthase from Streptomyces platensis
ComponentsEnt-copalyl diphosphate synthase
KeywordsISOMERASE / ent-copalyl diphosphate synthase / PtmT2 / structural genomics / APC109899 / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / PSI-Biology
Function / homologySqualene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / catalytic activity / Ent-copalyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces platensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsOsipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Rudolf, J.D. / Ma, M. / Chang, C.-Y. / Shen, B. / Joachimiak, A. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structure of the ent-Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene Synthase.
Authors: Rudolf, J.D. / Dong, L.B. / Cao, H. / Hatzos-Skintges, C. / Osipiuk, J. / Endres, M. / Chang, C.Y. / Ma, M. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ent-copalyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4367
Polymers54,8931
Non-polymers5426
Water9,548530
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ent-copalyl diphosphate synthase
hetero molecules

A: Ent-copalyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,87114
Polymers109,7862
Non-polymers1,08512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area3930 Å2
ΔGint-150 kcal/mol
Surface area38200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.870, 132.870, 190.748
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1274-

HOH

-
Components

#1: Protein Ent-copalyl diphosphate synthase /


Mass: 54893.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis (bacteria) / Gene: ptmT2 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A023VSF1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane buffer, 5 mM magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 59533 / Num. obs: 59533 / % possible obs: 99.4 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.026 / Rrim(I) all: 0.082 / Χ2: 1.361 / Net I/av σ(I): 32.596 / Net I/σ(I): 9.5 / Num. measured all: 545528
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.40.635227490.7810.290.7020.70893.3
1.83-1.865.90.55628670.8250.2420.610.72296.8
1.86-1.96.60.47529590.8850.1940.5150.74999.4
1.9-1.947.90.41829310.930.1570.4470.775100
1.94-1.988.70.34230230.9620.1220.3630.799100
1.98-2.039.70.28629830.9760.0960.3020.837100
2.03-2.08100.23829470.9840.0790.2510.893100
2.08-2.13100.19429580.9890.0640.2040.945100
2.13-2.2100.16929920.9910.0560.1780.975100
2.2-2.27100.14429770.9930.0480.1521.054100
2.27-2.35100.12429790.9950.0410.1311.117100
2.35-2.44100.11129920.9950.0370.1171.182100
2.44-2.55100.09930230.9960.0330.1041.249100
2.55-2.69100.08429630.9970.0280.0891.372100
2.69-2.86100.07729980.9970.0250.0811.518100
2.86-3.08100.06429880.9980.0210.0681.633100
3.08-3.399.90.0630250.9980.020.0631.829100
3.39-3.889.80.05930100.9980.020.0621.79599.9
3.88-4.889.60.05430440.9980.0180.0572.02499.8
4.88-509.40.05331250.9980.0180.0563.96699

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→42.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.131 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 2990 5 %RANDOM
Rwork0.1564 ---
obs0.1579 56537 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.19 Å2 / Biso mean: 27.101 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.29 Å20 Å2
2---0.59 Å20 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 1.8→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 29 530 4358
Biso mean--41.18 36.89 -
Num. residues----515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193969
X-RAY DIFFRACTIONr_bond_other_d0.0020.023655
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9725454
X-RAY DIFFRACTIONr_angle_other_deg0.82238409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.722.822163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1271534
X-RAY DIFFRACTIONr_chiral_restr0.0790.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_mcbond_it1.3242.0012073
X-RAY DIFFRACTIONr_mcbond_other1.32222072
X-RAY DIFFRACTIONr_mcangle_it2.0532.9922593
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 219 -
Rwork0.239 3859 -
all-4078 -
obs--93.04 %
Refinement TLS params.Method: refined / Origin x: -2.4477 Å / Origin y: -27.6468 Å / Origin z: -34.1819 Å
111213212223313233
T0.0526 Å20.0009 Å20.0112 Å2-0.0425 Å20.0022 Å2--0.005 Å2
L0.1043 °20.1532 °2-0.1285 °2-0.6644 °2-0.0733 °2--0.2327 °2
S-0.033 Å °-0.0342 Å °-0.0167 Å °-0.1128 Å °0.009 Å °-0.0179 Å °0.0091 Å °0.0285 Å °0.024 Å °

+
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