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- PDB-7hk8: Crystal Structure of N-methylhydantoinase in complex with 1-methy... -

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Basic information

Entry
Database: PDB / ID: 7hk8
TitleCrystal Structure of N-methylhydantoinase in complex with 1-methylimidazolidine-2,4-dione, C2221 form
ComponentsN-methylhydantoinase
KeywordsHYDROLASE / ATPASE / NMH / DHU / ATP-BINDING / CREATINE METABOLISM
Function / homology: / AMMONIUM ION
Function and homology information
Biological speciesGlutamicibacter protophormiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)285,61352
Polymers280,2482
Non-polymers5,36550
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-390 kcal/mol
Surface area85820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)257.410, 265.920, 120.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 1 through 1281 or resid 2000 through 2003))
21chain B

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
11METMETVALVAL(chain A and (resid 1 through 1281 or resid 2000 through 2003))AA1 - 12811 - 1281
12CACANH4NH4(chain A and (resid 1 through 1281 or resid 2000 through 2003))AC - E1301 - 1303
21METMETNH4NH4chain BBB - CA1 - 13031

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Components

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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

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Non-polymers , 5 types, 50 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
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 1.8M ammonium sulfate, 0.1M MES/NaOH pH 6.5, 3 %v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.8→49 Å / Num. obs: 101862 / % possible obs: 99.9 % / Redundancy: 6.792 % / Biso Wilson estimate: 68.69 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rrim(I) all: 0.177 / Χ2: 0.831 / Net I/σ(I): 11.29 / Num. measured all: 691846 / Scaling rejects: 44
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
2.8-2.876.9312.3390.8451712746074610.2952.529100
2.87-2.957.031.8261.1151069726872640.3871.97299.9
2.95-3.046.9991.3991.4449546707970790.5211.512100
3.04-3.136.9291.0361.9547562686568640.6551.12100
3.13-3.236.8110.7522.6845452667366730.7830.814100
3.23-3.356.5410.5233.7942489649764960.8730.568100
3.35-3.476.4140.3785.0939823621062090.9270.411100
3.47-3.617.0630.2757.2642569602760270.9610.297100
3.61-3.787.0110.2129.2340523578057800.9780.23100
3.78-3.966.9580.16411.7838316550755070.9850.178100
3.96-4.176.8470.12415.0536227529152910.9910.135100
4.17-4.436.3860.10217.5131750497449720.9930.111100
4.43-4.736.660.08321.4531207468746860.9950.09100
4.73-5.117.0350.0822.630786437743760.9960.087100
5.11-5.66.9340.08122.0128056404940460.9960.08899.9
5.6-6.266.6650.08121.3324462367136700.9960.088100
6.26-7.236.2840.06225.6820447325932540.9970.06899.8
7.23-8.856.7740.04237.6118913279327920.9990.045100
8.85-12.526.1210.03244.7713265216821670.9990.035100
12.52-45.26.1470.0345.577672128212480.9990.03297.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.21.1_5286refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.8→45.2 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.04 / Stereochemistry target values: ML / Details: C2221 form of NMH-complex
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 5130 5.04 %RANDOM
Rwork0.1922 96654 --
obs0.1941 101784 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.49 Å2 / Biso mean: 67.1302 Å2 / Biso min: 31.74 Å2
Refinement stepCycle: final / Resolution: 2.8→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19605 0 296 0 19901
Biso mean--101.44 --
Num. residues----2564
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12271X-RAY DIFFRACTION3.69TORSIONAL
12B12271X-RAY DIFFRACTION3.69TORSIONAL
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
2.8-2.830.40761500.363231753325
2.83-2.870.37061660.350131613327
2.87-2.90.36351890.33331883377
2.9-2.940.35831800.329931623342
2.94-2.980.41171520.344631893341
2.98-3.020.37191560.327232453401
3.02-3.060.3721770.316131443321
3.06-3.10.32241980.30931983396
3.1-3.150.3711800.29531853365
3.15-3.210.33111840.281232023386
3.21-3.260.30011530.262431953348
3.26-3.320.31271780.253831813359
3.32-3.380.30821840.248932163400
3.38-3.450.29231570.237232333390
3.45-3.530.25661520.221431833335
3.53-3.610.21511760.211132163392
3.61-3.70.26081530.18932433396
3.7-3.80.22831750.181832013376
3.8-3.910.22191680.166432183386
3.91-4.040.17731860.165831993385
4.04-4.180.22791660.158132413407
4.18-4.350.19721780.157632133391
4.35-4.550.18931990.149431983397
4.55-4.790.18691650.140632483413
4.79-5.090.16581550.140232383393
5.09-5.480.18771650.154132743439
5.48-6.030.21571680.165532683436
6.03-6.90.18131860.171332703456
6.9-8.680.17331640.150333223486
8.68-45.20.18681700.160634483618

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