[English] 日本語
Yorodumi
- PDB-4hac: Crystal Structure of the Mevalonate Kinase from an Archaeon Metha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hac
TitleCrystal Structure of the Mevalonate Kinase from an Archaeon Methanosarcina mazei
Components(Mevalonate kinase) x 2
KeywordsTRANSFERASE / GHMP / ATP binding / Phosphorylation
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Mevalonate kinase, archaeal / Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily ...Mevalonate kinase, archaeal / Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsZhuang, N. / Lee, K.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and preliminary X-ray diffraction analysis of mevalonate kinase from Methanosarcina mazei.
Authors: Zhuang, N. / Seo, K.H. / Chen, C. / Zhou, J. / Kim, S.W. / Lee, K.H.
History
DepositionSep 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mevalonate kinase
B: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6984
Polymers67,6492
Non-polymers492
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-36 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.295, 135.359, 45.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Mevalonate kinase /


Mass: 33801.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: MM_1762, MVK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PW39, mevalonate kinase
#2: Protein Mevalonate kinase /


Mass: 33847.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: MM_1762, MVK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PW39, mevalonate kinase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3350, MgCl2, pH 5.5, vapor diffusion, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.97947,0.97954,0.97179
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979471
20.979541
30.971791
ReflectionResolution: 1.91→50 Å / Num. obs: 47072 / % possible obs: 97.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.093 / Χ2: 1.111 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.91-1.945.90.70916881.207172.2
1.94-1.986.70.55123221.189198.4
1.98-2.026.80.48923451.205198.7
2.02-2.066.80.41223631.183199.6
2.06-2.16.80.32723731.183199.6
2.1-2.156.80.26223471.1591100
2.15-2.26.90.2323781.138199.8
2.2-2.266.90.20523851.134199.9
2.26-2.336.90.16923791.1331100
2.33-2.4170.14524001.1161100
2.41-2.4970.12923641.1581100
2.49-2.5970.11323871.112199.9
2.59-2.7170.10324251.1671100
2.71-2.857.10.0923931.1381100
2.85-3.037.10.08324091.0351100
3.03-3.277.20.08124450.964199.8
3.27-3.597.10.08424000.988199.6
3.59-4.1170.08824170.958198.6
4.11-5.186.60.07523770.968195.6
5.18-506.50.07424751.156194.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.92→40.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.964 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 2370 5 %RANDOM
Rwork0.2111 ---
obs0.2137 47017 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.41 Å2 / Biso mean: 41.5819 Å2 / Biso min: 21.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.92→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4537 0 2 166 4705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224604
X-RAY DIFFRACTIONr_angle_refined_deg1.951.9846235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94424.383162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06115791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.411526
X-RAY DIFFRACTIONr_chiral_restr0.1530.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213376
X-RAY DIFFRACTIONr_mcbond_it1.21.53052
X-RAY DIFFRACTIONr_mcangle_it2.05224898
X-RAY DIFFRACTIONr_scbond_it3.38531552
X-RAY DIFFRACTIONr_scangle_it5.4324.51336
LS refinement shellResolution: 1.915→1.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 165 -
Rwork0.337 3123 -
all-3288 -
obs--96.03 %
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)
12.8448-0.07340.64140.03470.00110.15560.1031-0.1588-0.0841-0.0334-0.0535-0.0290.0056-0.0509-0.04960.07780.0002-0.0070.14670.04240.085-1.0392-15.858820.5236
21.15670.14890.20720.122-0.12180.260.09110.0594-0.1744-0.0031-0.03070.00520.01790.0428-0.06040.13150.0336-0.04920.0818-0.03190.0898-48.1263-17.527412.4104
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 301
2X-RAY DIFFRACTION2B-6 - 301
3X-RAY DIFFRACTION2B601
4X-RAY DIFFRACTION2B701 - 811

+
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