[English] 日本語
Yorodumi
- PDB-3l8h: Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l8h
TitleCrystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from B. bronchiseptica complexed with magnesium and phosphate
ComponentsPutative haloacid dehalogenase-like hydrolase
KeywordsHYDROLASE / HAD superfamily / GMHB / D-glycero-D-manno-heptose-1 / 7-bisphosphate phosphatase
Function / homology
Function and homology information


D,D-heptose 1,7-bisphosphate phosphatase activity / D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
D,D-heptose 1,7-bisphosphate phosphatase / Histidinol-phosphate phosphatase / HAD-superfamily hydrolase,subfamily IIIA / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / beta-D-threo-hexo-2,4-diulo-2,5-furanose / PHOSPHATE ION / SARCOSINE / D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsNguyen, H. / Peisach, E. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Determinants of Substrate Recognition in the HAD Superfamily Member d-glycero-d-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB) .
Authors: Nguyen, H.H. / Wang, L. / Huang, H. / Peisach, E. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionDec 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative haloacid dehalogenase-like hydrolase
B: Putative haloacid dehalogenase-like hydrolase
C: Putative haloacid dehalogenase-like hydrolase
D: Putative haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,37022
Polymers77,1534
Non-polymers1,21718
Water12,538696
1
A: Putative haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5436
Polymers19,2881
Non-polymers2555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5685
Polymers19,2881
Non-polymers2804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6515
Polymers19,2881
Non-polymers3634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6086
Polymers19,2881
Non-polymers3205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.072, 58.389, 85.724
Angle α, β, γ (deg.)90.48, 97.54, 92.02
Int Tables number1
Space group name H-MP1

-
Components

-
Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
Putative haloacid dehalogenase-like hydrolase


Mass: 19288.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB4091, GMHB / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B-834 / References: UniProt: Q7WG29
#6: Sugar ChemComp-FX1 / beta-D-threo-hexo-2,4-diulo-2,5-furanose


Type: D-saccharide, beta linking / Mass: 178.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O6

-
Non-polymers , 6 types, 713 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-SAR / SARCOSINE / Sarcosine


Type: peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 0.1M Tris, 5mM Mg formate, 25% PEG 3350, 5% dioxane, 100mM sacrosine, pH 7.5, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2007
RadiationMonochromator: Si (1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 147263 / % possible obs: 94.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.68-1.742.40.253177.3
1.74-1.812.90.224189.9
1.81-1.893.30.186195.3
1.89-1.993.60.146196.3
1.99-2.123.70.114197
2.12-2.283.80.089197.3
2.28-2.513.80.073197.8
2.51-2.873.80.061198.2
2.87-3.623.80.047198.5
3.62-503.80.037199

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→29.174 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.19 / σ(F): 0 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 14317 9.72 %
Rwork0.1716 --
obs0.1743 147262 87.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.705 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.023 Å2-1.493 Å24.002 Å2
2---1.13 Å21.029 Å2
3---2.153 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 0 58 696 6082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085457
X-RAY DIFFRACTIONf_angle_d1.1277419
X-RAY DIFFRACTIONf_dihedral_angle_d16.4071980
X-RAY DIFFRACTIONf_chiral_restr0.07843
X-RAY DIFFRACTIONf_plane_restr0.005989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.69680.24552070.21032482X-RAY DIFFRACTION49
1.6968-1.71680.21753030.20922896X-RAY DIFFRACTION56
1.7168-1.73770.24983120.21293160X-RAY DIFFRACTION63
1.7377-1.75970.22283650.19573490X-RAY DIFFRACTION69
1.7597-1.78280.22833840.19193709X-RAY DIFFRACTION74
1.7828-1.80730.22874150.1944038X-RAY DIFFRACTION78
1.8073-1.83310.19243760.19184134X-RAY DIFFRACTION83
1.8331-1.86040.21414780.18824359X-RAY DIFFRACTION87
1.8604-1.88950.22714540.17734424X-RAY DIFFRACTION86
1.8895-1.92050.21994960.18154439X-RAY DIFFRACTION89
1.9205-1.95360.19414830.17474503X-RAY DIFFRACTION89
1.9536-1.98910.20765460.16714574X-RAY DIFFRACTION92
1.9891-2.02730.20344590.17064772X-RAY DIFFRACTION93
2.0273-2.06870.19575280.17124574X-RAY DIFFRACTION92
2.0687-2.11370.22845300.16494706X-RAY DIFFRACTION94
2.1137-2.16280.19944890.15134743X-RAY DIFFRACTION94
2.1628-2.21690.18945530.16414766X-RAY DIFFRACTION95
2.2169-2.27680.20225300.15974750X-RAY DIFFRACTION95
2.2768-2.34380.20095650.17184774X-RAY DIFFRACTION95
2.3438-2.41940.21845320.16474800X-RAY DIFFRACTION96
2.4194-2.50580.20375570.16794775X-RAY DIFFRACTION96
2.5058-2.60610.20485050.17184818X-RAY DIFFRACTION96
2.6061-2.72460.20925200.16914964X-RAY DIFFRACTION97
2.7246-2.86820.19025610.16624798X-RAY DIFFRACTION96
2.8682-3.04770.19445400.17534831X-RAY DIFFRACTION97
3.0477-3.28270.19015210.15964898X-RAY DIFFRACTION97
3.2827-3.61250.17375370.15044892X-RAY DIFFRACTION97
3.6125-4.1340.17525320.15014898X-RAY DIFFRACTION97
4.134-5.20360.18544910.15795024X-RAY DIFFRACTION99
5.2036-29.17820.19645480.19394955X-RAY DIFFRACTION98

+
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