[English] 日本語
Yorodumi
- PDB-6mlh: Crystal structure of X. citri phosphoglucomutase in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mlh
TitleCrystal structure of X. citri phosphoglucomutase in complex with GLUCOPYRANOSYL-1-METHYL-PHOSPHONIC ACID
ComponentsPhosphoglucomutase
KeywordsISOMERASE / enzyme / carbohydrate biosynthesis
Function / homology
Function and homology information


intramolecular phosphotransferase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III ...Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(1S)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol / Phosphoglucomutase
Similarity search - Component
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBeamer, L. / Stiers, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1409898 United States
CitationJournal: J.Org.Chem. / Year: 2019
Title: Inhibitory Evaluation of alpha PMM/PGM fromPseudomonas aeruginosa: Chemical Synthesis, Enzyme Kinetics, and Protein Crystallographic Study.
Authors: Zhu, J.S. / Stiers, K.M. / Soleimani, E. / Groves, B.R. / Beamer, L.J. / Jakeman, D.L.
History
DepositionSep 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_label_atom_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5003
Polymers51,2171
Non-polymers2822
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.571, 54.715, 172.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Phosphoglucomutase


Mass: 51217.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Gene: xanA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PGN7
#2: Sugar ChemComp-GPM / (1S)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol / GLUCOPYRANOSYL-1-METHYL-PHOSPHONIC ACID / Alpha-1 phosphonomethylene-D-glucopyranose


Type: D-saccharide / Mass: 258.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H15O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 8000, 0.2 M MgCl2, 0.1 M Hepes, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00001 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.65→57.56 Å / Num. obs: 50819 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.2
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.467 / Num. unique obs: 2496

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bmn

5bmn


Resolution: 1.65→46.22 Å / SU ML: 0.2154 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 21.8172
RfactorNum. reflection% reflection
Rfree0.2127 4806 5.02 %
Rwork0.1716 --
obs0.1737 50720 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.98 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 17 632 4055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063540
X-RAY DIFFRACTIONf_angle_d0.81114826
X-RAY DIFFRACTIONf_chiral_restr0.0513538
X-RAY DIFFRACTIONf_plane_restr0.0059640
X-RAY DIFFRACTIONf_dihedral_angle_d4.22222868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.31061600.32223082X-RAY DIFFRACTION99.2
1.67-1.690.29151510.31323020X-RAY DIFFRACTION100
1.69-1.710.3471600.29683078X-RAY DIFFRACTION99.94
1.71-1.730.34071750.2862962X-RAY DIFFRACTION99.9
1.73-1.750.28441890.26113015X-RAY DIFFRACTION99.88
1.75-1.780.3031250.2613047X-RAY DIFFRACTION100
1.78-1.80.26991670.23293046X-RAY DIFFRACTION99.88
1.8-1.830.2871550.23973045X-RAY DIFFRACTION100
1.83-1.860.23131400.22283018X-RAY DIFFRACTION99.91
1.86-1.890.25881840.22243092X-RAY DIFFRACTION99.94
1.89-1.920.25641500.22072983X-RAY DIFFRACTION99.81
1.92-1.960.25141700.2163052X-RAY DIFFRACTION99.88
1.96-1.990.24571470.20543058X-RAY DIFFRACTION99.88
1.99-2.030.22441460.19372998X-RAY DIFFRACTION99.94
2.03-2.080.241760.18543050X-RAY DIFFRACTION99.75
2.08-2.130.23921480.17972999X-RAY DIFFRACTION99.75
2.13-2.180.2241630.17423124X-RAY DIFFRACTION99.88
2.18-2.240.24171870.1812923X-RAY DIFFRACTION99.84
2.24-2.310.21821360.17893093X-RAY DIFFRACTION99.72
2.31-2.380.25841500.1773023X-RAY DIFFRACTION99.81
2.38-2.460.21441580.1663028X-RAY DIFFRACTION99.78
2.46-2.560.2231480.16183060X-RAY DIFFRACTION99.72
2.56-2.680.2031760.1583006X-RAY DIFFRACTION99.81
2.68-2.820.161730.15973010X-RAY DIFFRACTION99.75
2.82-30.22661570.15613029X-RAY DIFFRACTION99.56
3-3.230.21741370.15163062X-RAY DIFFRACTION99.56
3.23-3.550.18411660.143008X-RAY DIFFRACTION99.4
3.55-4.070.15041750.12943006X-RAY DIFFRACTION99.56
4.07-5.120.16321510.1223051X-RAY DIFFRACTION99.88
5.12-46.230.18911860.14813010X-RAY DIFFRACTION99.72
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)
11.148978744130.154939068260.1392393502342.799537149551.269875202122.92436000018-0.02302340206480.0874802898792-0.0596689748366-0.0849195702153-0.02289689889470.1370858997680.137991179151-0.01215546386210.04784844861420.1213884404070.02208155156410.01307178393090.136384554226-0.02698977334730.11863379669639.914306063337.65300256715.2537404822
20.2804208950490.0154419035127-0.1423622080310.843816348193-0.2179146667251.17826350154-0.009731781881420.02510348370430.01449284764130.0126421937118-0.000851630999542-0.02171066434010.009737411254930.01451883616340.007676493688520.07855515537170.001675641056670.007893967454090.131554745473-0.01476688945030.11706987233630.021605870454.168525556131.2263366182
31.104669486960.06299873192940.6071789584930.966373959499-0.04176305230792.576255137670.01023346309860.243516753762-0.162066191008-0.1401929287810.07370671983440.002043421068290.06012324585180.09171146942-0.05735583834430.1063768071263.29145619484E-50.01535396262860.125283021014-0.0347667560940.13346964884914.915403257863.465399309614.2917348798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 350 )
3X-RAY DIFFRACTION3chain 'A' and (resid 351 through 448 )

+
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