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- PDB-7hk5: Crystal Structure of N-methylhydantoinase in complex with 1-methy... -

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Basic information

Entry
Database: PDB / ID: 7hk5
TitleCrystal Structure of N-methylhydantoinase in complex with 1-methylimidazolidine-2,4-dione
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: 2.07 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)280,8029
Polymers280,2482
Non-polymers5547
Water28,9681608
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)219.380, 219.380, 135.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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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, 1615 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-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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1608 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 8-21 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.2 M Ammonium acetate, 0.1 M Bis-Tris/HCl pH 5.5, 25 %w/v PEG 3350, 3 %v/v TMAO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→49.6 Å / Num. obs: 198488 / % possible obs: 99.9 % / Redundancy: 14.109 % / Biso Wilson estimate: 33.86 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.284 / Rrim(I) all: 0.294 / Χ2: 0.868 / Net I/σ(I): 7.79 / Num. measured all: 2800486
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
2.07-2.1214.4033.9650.8420927514537145300.3234.11100
2.12-2.1814.3213.1671.0820309714188141820.4463.284100
2.18-2.2514.1372.3671.4419484413789137830.5772.456100
2.25-2.3113.4751.8371.8218069413413134100.6671.909100
2.31-2.3913.8161.442.3117975113011130100.7711.495100
2.39-2.4714.7881.1742.8918578312570125630.8441.21699.9
2.47-2.5714.6830.9153.5617869412172121700.8940.948100
2.57-2.6714.5740.7524.2917048711701116980.920.78100
2.67-2.7914.5010.5785.416325511260112580.9490.599100
2.79-2.9314.0090.4456.7315091410783107730.9650.46299.9
2.93-3.0913.4020.3348.2613714510245102330.9790.34799.9
3.09-3.2714.8370.25610.86143934971497010.9880.26599.9
3.27-3.514.6880.19513.53134112914791310.9920.20299.8
3.5-3.7814.4190.14916.67123170856585420.9950.15499.7
3.78-4.1413.7520.12318.73108046787378570.9960.12899.8
4.14-4.6312.5690.10120.6889984716671590.9960.10599.9
4.63-5.3414.0690.09422.5589143635963360.9970.09899.6
5.34-6.5513.7520.09821.674345541254060.9970.10299.9
6.55-9.2612.2120.08323.5252183427342730.9970.086100
9.26-49.612.790.07928.0231630250224730.9980.08298.8

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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: 2.07→49.6 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.45 / Stereochemistry target values: ML / Details: NMH bound at Ca2+ ion
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 9818 4.95 %RANDOM
Rwork0.1816 188395 --
obs0.1838 198213 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.69 Å2 / Biso mean: 40.259 Å2 / Biso min: 18.41 Å2
Refinement stepCycle: final / Resolution: 2.07→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19531 0 34 1608 21173
Biso mean--33.61 41.75 -
Num. residues----2552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119990
X-RAY DIFFRACTIONf_angle_d0.99427125
X-RAY DIFFRACTIONf_chiral_restr0.0593021
X-RAY DIFFRACTIONf_plane_restr0.0073611
X-RAY DIFFRACTIONf_dihedral_angle_d15.34211969
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
2.07-2.09350.37833500.347761686518
2.0935-2.11820.36123070.323761986505
2.1182-2.1440.3373170.318762106527
2.144-2.17110.38213350.317762166551
2.1711-2.19970.3323280.301761856513
2.1997-2.22980.33073160.281162036519
2.2298-2.26170.3353170.279662696586
2.2617-2.29550.32373290.266261966525
2.2955-2.33130.33473270.263362386565
2.3313-2.36950.32863210.248662416562
2.3695-2.41040.29873160.232162416557
2.4104-2.45420.26553410.217962336574
2.4542-2.50140.25383250.212262336558
2.5014-2.55250.25913320.205262506582
2.5525-2.6080.24733770.205262026579
2.608-2.66870.27443150.199962456560
2.6687-2.73540.25343500.199562426592
2.7354-2.80930.2613370.197162556592
2.8093-2.8920.23263150.189362846599
2.892-2.98530.23453170.183562666583
2.9853-3.0920.23893240.190162856609
3.092-3.21580.26473270.187262986625
3.2158-3.36210.24363310.186762756606
3.3621-3.53930.20983060.174963356641
3.5393-3.7610.1683360.151863066642
3.761-4.05130.17993040.140363466650
4.0513-4.45870.15553150.126363886703
4.4587-5.10340.14633210.120564006721
5.1034-6.42750.1953480.147264566804
6.4275-49.6140.15983340.140467317065

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