[English] 日本語
Yorodumi
- PDB-4iag: Crystal structure of ZbmA, the zorbamycin binding protein from St... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iag
TitleCrystal structure of ZbmA, the zorbamycin binding protein from Streptomyces flavoviridis
ComponentsZbm binding protein
KeywordsZorbamycin Binding Protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / BLMA_like / zorbamycin / reductive isopropylation
Function / homologyBleomycin resistance protein / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / response to antibiotic / Roll / Alpha Beta / Zbm binding protein
Function and homology information
Biological speciesStreptomyces flavoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Bigelow, L. / Bruno, C.J.P. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. ...Cuff, M.E. / Bigelow, L. / Bruno, C.J.P. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892.
Authors: Rudolf, J.D. / Bigelow, L. / Chang, C. / Cuff, M.E. / Lohman, J.R. / Chang, C.Y. / Ma, M. / Yang, D. / Clancy, S. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Structure summary
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Dec 2, 2015Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zbm binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,60410
Polymers15,0151
Non-polymers5899
Water99155
1
A: Zbm binding protein
hetero molecules

A: Zbm binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,20820
Polymers30,0312
Non-polymers1,17718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5910 Å2
ΔGint9 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.787, 38.787, 268.524
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsLikely forms a dimer with the crystallographic symmetry mate: x,y,z and 1-y, 1-x, 1/6-z.

-
Components

#1: Protein Zbm binding protein


Mass: 15015.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces flavoviridis (bacteria) / Strain: ATCC 21892 / Gene: zbmA / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: B9UIZ4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LYSINE RESIDUES IN THIS PROTEIN WERE SUBJECT TO REDUCTIVE ISOPROPYLATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: protein subject to reductive isopropylation, 0.8M Ammonium Sulfate, 0.1M Sodium Sitrate: HCl pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 3, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionRedundancy: 9.7 % / Av σ(I) over netI: 33.01 / Number: 101644 / Rmerge(I) obs: 0.068 / Χ2: 1.23 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 10484 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.165097.110.0572.1848.9
4.095.1699.710.0471.61510.6
3.584.0910010.051.52411.1
3.253.5810010.0551.5412
3.023.2510010.0671.4211.8
2.843.0210010.0741.14712.4
2.72.8410010.091.20212.2
2.582.710010.1051.10112.4
2.482.5810010.1181.15312.4
2.392.4810010.1171.02712.4
2.322.3910010.1290.98811.7
2.252.3210010.1781.20410.6
2.192.2510010.1860.989.8
2.142.1910010.2230.8989.4
2.092.1410010.2770.8478.2
2.052.0999.810.3150.9316.6
2.012.0597.910.3480.776
1.972.0195.410.3720.8675
1.931.9793.210.3970.8464.3
1.91.9387.510.4340.914
ReflectionResolution: 1.9→50 Å / Num. all: 10484 / Num. obs: 10484 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.225 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9340.4344600.91187.5
1.93-1.974.30.3974630.846193.2
1.97-2.0150.3724720.867195.4
2.01-2.0560.3485180.77197.9
2.05-2.096.60.3154960.931199.8
2.09-2.148.20.2775030.8471100
2.14-2.199.40.2235120.8981100
2.19-2.259.80.1865200.981100
2.25-2.3210.60.1785091.2041100
2.32-2.3911.70.1295150.9881100
2.39-2.4812.40.1175121.0271100
2.48-2.5812.40.1185351.1531100
2.58-2.712.40.1055211.1011100
2.7-2.8412.20.095241.2021100
2.84-3.0212.40.0745361.1471100
3.02-3.2511.80.0675451.421100
3.25-3.58120.0555391.541100
3.58-4.0911.10.055531.5241100
4.09-5.1610.60.0475871.615199.7
5.16-508.90.0576642.184197.1

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 44.75 Å / FOM : 0.172 / FOM acentric: 0.248 / FOM centric: 0 / Reflection: 9000 / Reflection acentric: 6258 / Reflection centric: 2742
Phasing MAD setR cullis acentric: 2.07 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 44.75 Å / Loc acentric: 0 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 6258 / Reflection centric: 2742
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.19-44.753.950.30.1653
7.05-12.192.230.10.174134
4.96-7.052.460.10213217
3.83-4.961.30.10.1432308
3.12-3.831.490.10746391
2.63-3.122.680.101113470
2.27-2.632.78001558548
2-2.272.38002116621
Phasing MAD set siteAtom type symbol: Se / B iso: 53.9197 / Fract x: 0.914 / Fract y: 0.714 / Fract z: 0.017 / Occupancy: 4.23 / Occupancy iso: 0
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.19-44.750.0410.406059653
7.05-12.190.1650.463020874134
4.96-7.050.2610.5270430213217
3.83-4.960.250.4280740432308
3.12-3.830.2750.41801137746391
2.63-3.120.250.355015831113470
2.27-2.630.1560.211021061558548
2-2.270.0650.084027372116621
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 10313
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.58-10073.90.488506
4.35-5.5870.60.807506
3.76-4.3569.50.829506
3.39-3.7670.40.825503
3.14-3.39720.803502
2.94-3.1469.80.777507
2.78-2.9470.50.767505
2.65-2.7872.20.751509
2.54-2.6576.30.735501
2.45-2.5481.30.745506
2.37-2.4579.20.685511
2.3-2.3781.20.719502
2.23-2.384.90.747507
2.18-2.2380.80.754512
2.12-2.1891.60.777522
2.08-2.1282.50.698506
2.03-2.0885.20.71515
1.99-2.0387.20.684501
1.95-1.9991.50.633507
1.9-1.9588.70.565679

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2317 / WRfactor Rwork: 0.1832 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8678 / SU B: 7.7 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1613 / SU Rfree: 0.1483 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.148
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 492 4.8 %RANDOM
Rwork0.1893 ---
all0.1913 10243 --
obs0.1913 10243 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.97 Å2 / Biso mean: 38.2635 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.57 Å20 Å2
2--0.57 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 38 55 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191021
X-RAY DIFFRACTIONr_bond_other_d0.0050.02968
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9671379
X-RAY DIFFRACTIONr_angle_other_deg1.3983.0112219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80123.8347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40315140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.541157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 36 -
Rwork0.285 639 -
all-675 -
obs--90 %
Refinement TLS params.Method: refined / Origin x: 46.1737 Å / Origin y: -2.9324 Å / Origin z: 32.3225 Å
111213212223313233
T0.1502 Å2-0.1359 Å20.0278 Å2-0.1598 Å20.0037 Å2--0.062 Å2
L1.9312 °20.6523 °20.1694 °2-1.7258 °20.2261 °2--1.4975 °2
S0.2655 Å °-0.3032 Å °0.0669 Å °0.1092 Å °-0.2601 Å °0.0033 Å °0.056 Å °0.0276 Å °-0.0054 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