[English] 日本語
Yorodumi
- PDB-6mtz: Crystal structure of an uncharacterized protein from Helicobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mtz
TitleCrystal structure of an uncharacterized protein from Helicobacter pylori G27
ComponentsHepC.19480.a.B1
KeywordsUNKNOWN FUNCTION / SSGCID / Structural Genomics / Helicobacter pylori / uncharacterized protein / Seattle Structural Genomics Center for Infectious Disease
Function / homology: / DHH phosphoesterase superfamily / IODIDE ION / Phosphoesterase
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of an uncharacterized protein from Helicobacter pylori G27
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HepC.19480.a.B1
B: HepC.19480.a.B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,75043
Polymers82,3672
Non-polymers4,38341
Water5,639313
1
A: HepC.19480.a.B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,72524
Polymers41,1831
Non-polymers2,54123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HepC.19480.a.B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,02519
Polymers41,1831
Non-polymers1,84218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.730, 66.740, 200.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HepC.19480.a.B1


Mass: 41183.301 Da / Num. of mol.: 2 / Fragment: HepyC.19480.a.B11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: HPG27_386
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B5Z6F2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG1 screen, F3: 200mM Ammonium citrate dibasic pH 5, 20% PEG3350: HepyC.18480.a.B11.PW38477 at 31.62mg/ml. For phasing, a crysta was incubated for 10sec each in reservoir 10% 2. ...Details: Microlytic MCSG1 screen, F3: 200mM Ammonium citrate dibasic pH 5, 20% PEG3350: HepyC.18480.a.B11.PW38477 at 31.62mg/ml. For phasing, a crysta was incubated for 10sec each in reservoir 10% 2.5M NaI in EG and 20% 2.5M NaI in EG (500mM final NaI concentration), and directly vitrified. Tray 301766f3, puck OVZ1-5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 14, 2018
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→44.943 Å / Num. obs: 45317 / % possible obs: 100 % / Redundancy: 13.491 % / Biso Wilson estimate: 39.517 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.101 / Χ2: 1.002 / Net I/σ(I): 17.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.218.2850.6063.4932810.8460.647100
2.21-2.2710.8050.5214.7132040.9030.547100
2.27-2.3313.980.4376.431420.9550.453100
2.33-2.414.4070.3777.4230390.9680.39100
2.4-2.4814.4180.3517.9329480.9710.364100
2.48-2.5714.4450.2899.4528820.9810.299100
2.57-2.6714.4390.24111.2427630.9850.25100
2.67-2.7814.4670.18914.0726530.9920.196100
2.78-2.914.430.1616.325720.9940.166100
2.9-3.0414.3880.13518.8324400.9950.14100
3.04-3.2114.3620.10423.6123420.9970.108100
3.21-3.414.2490.08927.4122160.9980.092100
3.4-3.6314.160.07431.6620810.9980.077100
3.63-3.9314.0150.06634.5919790.9990.069100
3.93-4.313.9550.0637.6318000.9990.06299.9
4.3-4.8113.8470.05838.2616460.9990.06100
4.81-5.5513.7750.06235.6114790.9990.06499.9
5.55-6.813.3210.06933.0912540.9980.072100
6.8-9.6212.8340.05337.2110020.9990.05599.8
9.62-44.94311.7190.04939.485940.9990.05197.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.15→44.943 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.53
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 2002 4.42 %0
Rwork0.1754 ---
obs0.1777 45246 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 218.14 Å2 / Biso mean: 43.7096 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 2.15→44.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 62 316 5765
Biso mean--56.81 41.99 -
Num. residues----691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095540
X-RAY DIFFRACTIONf_angle_d0.7537509
X-RAY DIFFRACTIONf_dihedral_angle_d12.9413259
X-RAY DIFFRACTIONf_chiral_restr0.045827
X-RAY DIFFRACTIONf_plane_restr0.004986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1501-2.20380.3071440.211130153159
2.2038-2.26340.28811280.202330563184
2.2634-2.330.27831240.191430503174
2.33-2.40520.2321560.182730353191
2.4052-2.49120.27021420.191430473189
2.4912-2.59090.26241310.191830733204
2.5909-2.70880.26221280.186330503178
2.7088-2.85160.23511290.18830933222
2.8516-3.03020.24461300.198731203250
3.0302-3.26410.22521630.18430303193
3.2641-3.59250.21251720.171731023274
3.5925-4.1120.21351380.144831213259
4.112-5.17950.17681660.141731323298
5.1795-44.95250.23761510.19333203471
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)
12.8593-0.48820.38052.81080.19942.13690.09090.15420.2213-0.4094-0.22960.4563-0.5576-0.5470.09860.33050.0971-0.06260.3459-0.05650.284948.812926.353937.5442
20.80950.0203-0.35372.11360.7161.71050.0017-0.05430.0902-0.02590.0543-0.018-0.14320.0541-0.04420.1702-0.01080.00610.17230.01330.14462.362414.653740.5219
32.81251.15510.43824.64091.37254.59180.04040.1566-0.3621-0.4165-0.01740.1980.2898-0.2562-0.0040.32630.0188-0.09380.35820.03590.3546.37043.601213.8881
42.76190.2268-1.09673.4315-0.96743.7316-0.10770.50150.1541-0.1035-0.1055-0.1751-0.23440.28390.17910.2916-0.0552-0.02780.31420.05790.18681.25252.47945.8605
52.93070.6442-0.55743.0301-0.83542.7998-0.17951.08980.0263-0.60430.15560.06280.15150.06580.10390.4085-0.0732-0.01090.5568-0.0090.274778.3701-3.0677-2.6405
62.11160.8260.25882.19921.00662.4693-0.13330.0146-0.0477-0.19750.043-0.03680.13590.09880.06870.19790.03080.02620.16760.04350.221176.3721-2.158423.4614
72.13330.2473-0.92417.7993-0.36426.5290.00490.00260.94070.03320.1294-0.1297-0.58680.1016-0.07910.3335-0.023-0.06190.30590.05490.588986.148225.773420.9134
82.76510.26880.17064.40080.57423.81340.00330.21631.0909-0.03430.10260.7251-0.8821-0.3931-0.15870.73010.11570.03790.48670.14770.853481.042431.796615.414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 96 )A0 - 96
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 245 )A97 - 245
3X-RAY DIFFRACTION3chain 'A' and (resid 246 through 347 )A246 - 347
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 51 )B0 - 51
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 133 )B52 - 133
6X-RAY DIFFRACTION6chain 'B' and (resid 134 through 245 )B134 - 245
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 291 )B246 - 291
8X-RAY DIFFRACTION8chain 'B' and (resid 292 through 346 )B292 - 346

+
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