[English] 日本語
Yorodumi
- PDB-3ext: Crystal structure of KGPDC from Streptococcus mutans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ext
TitleCrystal structure of KGPDC from Streptococcus mutans
ComponentsRmpD (Hexulose-6-phosphate synthase)
KeywordsLYASE / beta barrel
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / carbohydrate metabolic process
Similarity search - Function
HPS/KGPDC domain / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLiu, X. / Li, G.L. / Li, L.F. / Su, X.D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Open-closed conformational change revealed by the crystal structures of 3-keto-L-gulonate 6-phosphate decarboxylase from Streptococcus mutans
Authors: Li, G.L. / Liu, X. / Nan, J. / Brostromer, E. / Li, L.F. / Su, X.D.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RmpD (Hexulose-6-phosphate synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8752
Polymers23,8501
Non-polymers241
Water1,47782
1
A: RmpD (Hexulose-6-phosphate synthase)
hetero molecules

A: RmpD (Hexulose-6-phosphate synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7494
Polymers47,7002
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2390 Å2
ΔGint-23.7 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.780, 83.780, 171.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

21A-297-

HOH

-
Components

#1: Protein RmpD (Hexulose-6-phosphate synthase) / 3-keto-L-gulonate 6-phosphate decarboxylase


Mass: 23850.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: ulaD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93DA8, 3-dehydro-L-gulonate-6-phosphate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M KCl, 0.05M HEPES, pH7.5, 35%(v/v) pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9074 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9074 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 20739 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.447 Å2 / Rmerge(I) obs: 0.055
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.120.3458.351319325898.3
2.12-2.270.21213.650449311899.9
2.27-2.450.14819.246560288799.7
2.45-2.680.09828.143274269799.7
2.68-30.06838.738852245599.8
3-3.460.0485033900216999.7
3.46-4.220.03561.428541187499.8
4.22-5.910.03965.221552148499.2
5.910.03257.2935479785.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.589 / Cor.coef. Fo:Fc: 0.587
Highest resolutionLowest resolution
Rotation2 Å28.63 Å
Translation2 Å28.63 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KV8

1kv8


Resolution: 2→19.75 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.847 / SU B: 6.565 / SU ML: 0.094 / SU R Cruickshank DPI: 0.15 / SU Rfree: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1042 5 %RANDOM
Rwork0.199 ---
obs0.2 19853 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.61 Å2 / Biso mean: 29.087 Å2 / Biso min: 13.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 1 82 1662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221603
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9472173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25925.07765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35715269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.25158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021188
X-RAY DIFFRACTIONr_nbd_refined0.2040.2701
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.281
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.210
X-RAY DIFFRACTIONr_mcbond_it0.9581.51074
X-RAY DIFFRACTIONr_mcangle_it1.45521655
X-RAY DIFFRACTIONr_scbond_it2.3033629
X-RAY DIFFRACTIONr_scangle_it3.2674.5518
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 77 -
Rwork0.242 1429 -
all-1506 -
obs--99.93 %
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)
10.5861-0.7766-0.03151.0382-0.07751.57160.2265-0.00310.0972-0.1441-0.0595-0.02530.0650.2027-0.1670.0410.03830.01490.0285-0.02520.089710.844639.206326.0476
20.2526-0.1032-0.60935.62871.1591.61760.47440.3743-0.0335-0.676-0.3519-0.07620.0830.1282-0.12250.19670.1925-0.00770.0981-0.0418-0.018110.314833.604412.2769
31.6969-0.0006-0.22573.7285-0.42291.24630.48420.2566-0.1516-0.5028-0.3688-0.1180.27780.152-0.11540.19110.2336-0.03780.1149-0.0851-0.014915.038526.922412.2115
43.0655-2.5279-2.57713.5750.91253.1530.12350.1258-0.1619-0.0522-0.17510.33640.56440.33670.05170.17270.1539-0.0903-0.0064-0.11490.108115.56219.565625.8154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 129
2X-RAY DIFFRACTION2A130 - 155
3X-RAY DIFFRACTION3A156 - 192
4X-RAY DIFFRACTION4A193 - 221

+
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