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- PDB-4yt2: Hmd II from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 4yt2
TitleHmd II from Methanocaldococcus jannaschii
ComponentsH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
KeywordsMETAL BINDING PROTEIN / Rossmann-fold / oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein / Hmd, C-terminal helical subdomain / Methenyltetrahydromethanopterin dehydrogenase, Hmd-type / H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal / HMD, C-terminal domain superfamily / H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein / Hmd, C-terminal helical subdomain / Methenyltetrahydromethanopterin dehydrogenase, Hmd-type / H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal / HMD, C-terminal domain superfamily / H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
Funding support Japan, Germany, 2items
OrganizationGrant numberCountry
JST-PRESTO Japan
Max Planck Society Germany
CitationJournal: Febs J. / Year: 2015
Title: Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs.
Authors: Fujishiro, T. / Ataka, K. / Ermler, U. / Shima, S.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
B: H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1676
Polymers74,6982
Non-polymers4694
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12960 Å2
ΔGint-104 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.520, 77.810, 153.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: HIS / End label comp-ID: HIS

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNchain AAA11 - 3534 - 346
2LYSLYSchain BBB8 - 3531 - 346

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Components

#1: Protein H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338


Mass: 37349.125 Da / Num. of mol.: 2 / Fragment: Rossmann-like domain, unp residues 8-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ1338 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58734
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 40% (v/v) PEG 300, 100 mM phosphate-citrate buffer

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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: Jul 26, 2011
RadiationMonochromator: A double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 76381 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 25.92 Å2 / Rmerge F obs: 0.08 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.072 / Χ2: 1.056 / Net I/σ(I): 12.08 / Num. measured all: 373503
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.65-1.70.6050.5652.9432899646464620.632100
1.7-1.80.4060.3984.155454410893108880.447100
1.8-20.1970.2077.187835715836158120.23499.8
2-2.40.0820.10412.118781818015179510.11899.6
2.4-30.0460.06717.145805412190121290.07699.5
3-3.80.0340.05621.9931668658265590.06299.7
3.8-4.90.030.04924.7515522346234230.05598.9
4.9-80.0270.04328.1611103239823860.04999.5
8-120.0220.0430.8624575385250.04597.6
120.0230.03629.9510812632460.04193.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-HmdII from M. jannaschii

Resolution: 1.65→43.532 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 3832 5.02 %
Rwork0.1802 72479 -
obs0.1821 76311 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.43 Å2 / Biso mean: 34.4761 Å2 / Biso min: 13.6 Å2
Refinement stepCycle: final / Resolution: 1.65→43.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 31 321 5560
Biso mean--52.63 41.37 -
Num. residues----689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125325
X-RAY DIFFRACTIONf_angle_d1.4347192
X-RAY DIFFRACTIONf_chiral_restr0.07855
X-RAY DIFFRACTIONf_plane_restr0.008914
X-RAY DIFFRACTIONf_dihedral_angle_d13.9962011
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3054X-RAY DIFFRACTION7.014TORSIONAL
12B3054X-RAY DIFFRACTION7.014TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67090.37741460.290526292775100
1.6709-1.69290.31091300.279327162846100
1.6929-1.71610.30951250.25226072732100
1.7161-1.74060.28241320.252826932825100
1.7406-1.76660.25261430.240626582801100
1.7666-1.79420.28351420.233426362778100
1.7942-1.82360.29181350.226226782813100
1.8236-1.8550.3121360.21726432779100
1.855-1.88880.23341430.205526722815100
1.8888-1.92510.24381510.19426392790100
1.9251-1.96440.21291470.193226392786100
1.9644-2.00710.24211470.186126932840100
2.0071-2.05380.23741530.184526402793100
2.0538-2.10520.20171290.181227192848100
2.1052-2.16210.19771340.179926492783100
2.1621-2.22570.20261340.18492694282899
2.2257-2.29750.25581340.18642656279099
2.2975-2.37960.20511530.180326772830100
2.3796-2.47490.24431400.179626772817100
2.4749-2.58750.21411130.178627172830100
2.5875-2.72390.21771470.17626802827100
2.7239-2.89460.22121600.18322671283199
2.8946-3.1180.2241600.180627032863100
3.118-3.43170.21261490.179926932842100
3.4317-3.92790.19821310.158127672898100
3.9279-4.94770.17671540.14962741289599
4.9477-43.54670.21671640.18172892305699
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)
12.3733-0.1351-1.79621.78320.10156.32350.0025-0.1058-0.04680.07780.0225-0.02360.26050.1429-0.00540.15570.0071-0.01970.109500.16423.038-44.9965-13.8644
24.05780.61580.73937.4801-0.03782.34150.078-0.08740.34390.142-0.004-0.486-0.19350.1457-0.05620.1382-0.00840.02420.1645-0.00720.218629.3368-30.7191-26.0592
31.395-0.7898-0.27462.6410.41420.68180.054-0.0578-0.0697-0.0067-0.07090.223-0.0111-0.06630.02570.1242-0.017-0.01030.1753-0.00570.20579.3419-27.6346-25.3173
42.0033-0.217-1.06911.56310.33982.4593-0.0836-0.1666-0.1480.23290.0020.16230.0752-0.04440.05230.1904-0.00350.00260.12620.01980.203311.1365-8.9158-15.4346
54.24542.0741-0.3655.8543-0.46762.2980.20030.14160.39150.0003-0.06010.5614-0.2697-0.3174-0.10920.25190.06320.0470.2498-0.02040.2494-12.289214.7341-16.3138
67.1551-0.8448-3.72563.7445-0.70944.6550.1140.4935-0.2524-0.1554-0.10370.11350.0218-0.4128-0.02490.2663-0.0067-0.00590.1855-0.020.15374.163113.4596-23.417
74.52574.9751-3.78164.5835-3.74412.8966-0.0004-0.2291-0.0999-0.0828-0.1118-0.1814-0.0170.07960.0610.2754-0.0362-0.00180.1883-0.00780.21482.706511.3864-15.6608
85.4999-1.0002-2.74685.645-0.3933.38140.0557-0.33280.01480.215-0.0385-0.0584-0.21080.1806-0.06810.2105-0.0346-0.03540.20840.01020.09417.13469.1959-9.7111
91.56560.1054-0.39642.30880.31095.2468-0.0944-0.1079-0.15640.3012-0.0979-0.03490.52310.16730.18380.2054-0.00410.0510.13540.01490.222710.3083-17.5632-15.6539
108.1346-0.0744-2.61584.44082.70838.8324-0.3013-0.4475-0.5960.8553-0.14920.56791.09010.1020.36170.4341-0.020.17170.21460.05180.5861.424-27.4358-13.1895
117.79894.28660.19544.8918-0.71715.276-0.23720.72240.4161-0.26790.28380.75890.0971-0.8223-0.08870.23530.0706-0.02410.2302-0.03060.36391.4604-19.3408-31.2197
128.7649-1.3989-1.21094.9547-0.62633.3601-0.04650.33280.35270.0319-0.0429-0.1634-0.27750.24540.12210.1918-0.0357-0.00140.1477-0.04330.164220.42-0.1287-27.7339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 92 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 153 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 240 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 353 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 92 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 93 through 142 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 143 through 166 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 213 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 214 through 271 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 272 through 300 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 301 through 322 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 323 through 353 )B0

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