[English] 日本語
Yorodumi
- PDB-7hk6: Crystal Structure of N-methylhydantoinase in complex with 1-methy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7hk6
TitleCrystal Structure of N-methylhydantoinase in complex with 1-methylimidazolidine-2,4-dione, iodide soak
ComponentsN-methylhydantoinase
KeywordsHYDROLASE / ATPASE / NMH / DHU / ATP-BINDING / CREATINE METABOLISM
Function / homology: / IODIDE ION / AMMONIUM ION
Function and homology information
Biological speciesGlutamicibacter protophormiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsStihle, M. / Benz, J. / Asztalos, P. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a N-methylhydantoinase complex
Authors: Asztalos, P. / Meier, T. / Clairfeuille, T. / Rudolph, M.G.
History
DepositionOct 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-methylhydantoinase
B: N-methylhydantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,75148
Polymers280,2482
Non-polymers5,50346
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)217.790, 217.790, 133.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 1:257 or resid 259:534 or resid...
21(chain B and (resid 1:257 or resid 259:388 or resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and (resid 1:257 or resid 259:534 or resid...AA1 - 2571 - 257
12PROPROALAALA(chain A and (resid 1:257 or resid 259:534 or resid...AA259 - 534259 - 534
13ARGARGPHEPHE(chain A and (resid 1:257 or resid 259:534 or resid...AA536 - 631536 - 631
14GLNGLNGLYGLY(chain A and (resid 1:257 or resid 259:534 or resid...AA633 - 635633 - 635
15PROPROVALVAL(chain A and (resid 1:257 or resid 259:534 or resid...AA637 - 692637 - 692
16LYSLYSILEILE(chain A and (resid 1:257 or resid 259:534 or resid...AA698 - 861698 - 861
17HISHISPHEPHE(chain A and (resid 1:257 or resid 259:534 or resid...AA863 - 981863 - 981
18GLYGLYARGARG(chain A and (resid 1:257 or resid 259:534 or resid...AA983 - 1098983 - 1098
19ASPASPLEULEU(chain A and (resid 1:257 or resid 259:534 or resid...AA1100 - 12301100 - 1230
110ARGARGTHRTHR(chain A and (resid 1:257 or resid 259:534 or resid...AA1232 - 12481232 - 1248
111ALAALAARGARG(chain A and (resid 1:257 or resid 259:534 or resid...AA1250 - 12771250 - 1277
112ASNASNALAALA(chain A and (resid 1:257 or resid 259:534 or resid...AA1279 - 12801279 - 1280
21METMETLYSLYS(chain B and (resid 1:257 or resid 259:388 or resid...BB1 - 2571 - 257
22PROPROLEULEU(chain B and (resid 1:257 or resid 259:388 or resid...BB259 - 388259 - 388
23METMETALAALA(chain B and (resid 1:257 or resid 259:388 or resid...BB395 - 534395 - 534
24ARGARGPHEPHE(chain B and (resid 1:257 or resid 259:388 or resid...BB536 - 631536 - 631
25GLNGLNGLYGLY(chain B and (resid 1:257 or resid 259:388 or resid...BB633 - 635633 - 635
26PROPROVALVAL(chain B and (resid 1:257 or resid 259:388 or resid...BB637 - 692637 - 692
27LYSLYSILEILE(chain B and (resid 1:257 or resid 259:388 or resid...BB698 - 861698 - 861
28HISHISPHEPHE(chain B and (resid 1:257 or resid 259:388 or resid...BB863 - 981863 - 981
29GLYGLYARGARG(chain B and (resid 1:257 or resid 259:388 or resid...BB983 - 1098983 - 1098
210ASPASPLEULEU(chain B and (resid 1:257 or resid 259:388 or resid...BB1100 - 12301100 - 1230
211ARGARGTHRTHR(chain B and (resid 1:257 or resid 259:388 or resid...BB1232 - 12481232 - 1248
212ALAALAARGARG(chain B and (resid 1:257 or resid 259:388 or resid...BB1250 - 12771250 - 1277
213ASNASNALAALA(chain B and (resid 1:257 or resid 259:388 or resid...BB1279 - 12801279 - 1280

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein N-methylhydantoinase


Mass: 140124.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glutamicibacter protophormiae (bacteria)
Plasmid: pBP010 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101

-
Non-polymers , 6 types, 419 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1BC1 / 1-methylimidazolidine-2,4-dione


Mass: 114.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#5: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 9.4 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.1 M Bis-Tris/HCl pH 5.5, 25% PEG 3350, 0.2 M ammonium sulfate, 3 %w/v TMAO, 5 %w/v DDM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.77003 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77003 Å / Relative weight: 1
ReflectionResolution: 2.62→49.12 Å / Num. obs: 96326 / % possible obs: 100 % / Redundancy: 14.566 % / Biso Wilson estimate: 52.95 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.334 / Rrim(I) all: 0.346 / Χ2: 0.916 / Net I/σ(I): 8.27 / Num. measured all: 1403072 / Scaling rejects: 48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.62-2.6914.6383.430.79103039703970390.3543.554100
2.69-2.7614.4272.9260.9498562683368320.3963.033100
2.76-2.8413.7322.3151.2391700667866780.4932.404100
2.84-2.9314.1271.8041.6591374646864680.6211.872100
2.93-3.0315.0931.3652.3495585633463330.7631.413100
3.03-3.1315.0331.0683.0991037605660560.8391.105100
3.13-3.2514.9080.7954.1988119591359110.9160.823100
3.25-3.3814.8130.6145.4683620564556450.9440.636100
3.38-3.5313.9540.466.9976316546954690.9660.478100
3.53-3.7114.2510.3528.874801524952490.9780.365100
3.71-3.9115.5140.27311.1876548493449340.9880.282100
3.91-4.1415.3150.21213.6172225471647160.9920.22100
4.14-4.4315.060.17315.7767199446244620.9940.179100
4.43-4.7814.5280.15317.2760102413741370.9950.158100
4.78-5.2413.290.15616.0951021384038390.9940.162100
5.24-5.8615.2720.16416.4753191348234830.9940.169100
5.86-6.7615.1340.15916.8546811309430930.9940.165100
6.76-8.2914.3240.10422.3338216266826680.9970.108100
8.29-11.7212.9480.06829.3727088209220920.9980.071100
11.72-49.12113.5170.0632.0616518125012220.9990.06397.8

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_2363refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.62→49.121 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.76 / Stereochemistry target values: ML / Details: iodide soak for SIRAS phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 4702 4.89 %RANDOM
Rwork0.1821 91494 --
obs0.1846 96196 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.13 Å2 / Biso mean: 53.7913 Å2 / Biso min: 17.5 Å2
Refinement stepCycle: final / Resolution: 2.62→49.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19531 0 73 373 19977
Biso mean--83.25 43.13 -
Num. residues----2552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819978
X-RAY DIFFRACTIONf_angle_d0.99827125
X-RAY DIFFRACTIONf_chiral_restr0.0583021
X-RAY DIFFRACTIONf_plane_restr0.0073611
X-RAY DIFFRACTIONf_dihedral_angle_d14.35711969
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11873X-RAY DIFFRACTION5.867TORSIONAL
12B11873X-RAY DIFFRACTION5.867TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.62-2.64980.40131610.368929743135
2.6498-2.6810.40481570.348230153172
2.681-2.71360.43731660.341229803146
2.7136-2.7480.41651560.320230063162
2.748-2.78410.33371660.300529983164
2.7841-2.82230.31491610.283529933154
2.8223-2.86260.35341450.282530163161
2.8626-2.90530.31191710.254330343205
2.9053-2.95070.32551450.247330223167
2.9507-2.99910.30781410.249730153156
2.9991-3.05080.30481470.249330273174
3.0508-3.10630.37331550.245830243179
3.1063-3.1660.30751750.232430063181
3.166-3.23060.25731480.235530433191
3.2306-3.30080.3161510.228630273178
3.3008-3.37760.27991520.206230273179
3.3776-3.4620.24921680.196630353203
3.462-3.55560.21461420.182230453187
3.5556-3.66020.21641640.168930323196
3.6602-3.77830.22011770.156530343211
3.7783-3.91330.20791270.148830903217
3.9133-4.06990.19451540.143830423196
4.0699-4.25510.18051500.133330803230
4.2551-4.47920.17191540.128330733227
4.4792-4.75970.17821570.121730533210
4.7597-5.12680.1621570.130831033260
5.1268-5.64210.20221670.141730933260
5.6421-6.45690.19661640.153431213285
6.4569-8.12910.18711710.158731503321
8.1291-49.12920.18361530.168233363489

+
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