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- PDB-4yt8: SeMet-labelled HmdII from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 4yt8
TitleSeMet-labelled HmdII from Methanocaldococcus jannaschii
ComponentsH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
KeywordsMETAL BINDING PROTEIN / Rossmann-like fold / [Fe]-hydrogenase paralog
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
TRIETHYLENE GLYCOL / H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.902 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

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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)82,5103
Polymers82,3592
Non-polymers1501
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-110 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.570, 77.970, 153.650
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA10 - 353
211chain BB10 - 353

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Components

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


Mass: 41179.684 Da / Num. of mol.: 2 / Fragment: Rossmann-like domain, UNP residues 1-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ1338 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 35% (v/v) PEG 300 and 100 mM phosphate-citrate buffer

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9791
SYNCHROTRONSLS X10SA20.9798
SYNCHROTRONSLS X10SA30.972
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELApr 25, 2013
DECTRIS PILATUS 6M2PIXELApr 25, 2013
DECTRIS PILATUS 6M3PIXELApr 25, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1A double-crystal Si(111) monochromatorMADMx-ray1
2A double-crystal Si(111) monochromatorMADMx-ray2
3A double-crystal Si(111) monochromatorMADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97981
30.9721
ReflectionResolution: 1.9→50 Å / Num. obs: 50381 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 27.43 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.127 / Χ2: 1.393 / Net I/σ(I): 11.8 / Num. measured all: 276025
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-23.90.9580.5862.228611816584165770.38695.7
2.6-2.90.9780.2111.55164910361103580.236100
2.9-3.10.9870.15216.0125935485848580.169100
3.1-3.40.9910.12519.2427646527252720.139100
3.4-3.80.9920.10322.7523131471947160.11699.9
3.8-4.30.9930.09327.0219568371337120.103100
4.3-5.90.9950.08227.4825516504550420.09199.9
5.9-80.9960.07628.1610144190519050.084100
8-120.9970.05533.2442849009000.062100
120.9870.06535.2620343933850.07298

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.902→43.588 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 2556 5.08 %
Rwork0.1849 47745 -
obs0.1864 50301 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.45 Å2 / Biso mean: 30.8366 Å2 / Biso min: 11.84 Å2
Refinement stepCycle: final / Resolution: 1.902→43.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 10 224 5434
Biso mean--40.06 35.87 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085295
X-RAY DIFFRACTIONf_angle_d1.1937158
X-RAY DIFFRACTIONf_chiral_restr0.051851
X-RAY DIFFRACTIONf_plane_restr0.005914
X-RAY DIFFRACTIONf_dihedral_angle_d13.9391993
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2914X-RAY DIFFRACTION8.829TORSIONAL
12B2914X-RAY DIFFRACTION8.829TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9021-1.93870.37281450.30472450259594
1.9387-1.97820.31331420.268226062748100
1.9782-2.02120.29331420.241826512793100
2.0212-2.06830.28691340.219525832717100
2.0683-2.120.23881410.202226482789100
2.12-2.17730.25931450.19726152760100
2.1773-2.24140.24491240.199126572781100
2.2414-2.31370.26061500.196126312781100
2.3137-2.39640.27131370.186426472784100
2.3964-2.49230.21531250.189326732798100
2.4923-2.60580.20711330.180126402773100
2.6058-2.74310.25441450.189626502795100
2.7431-2.91490.19781460.18426652811100
2.9149-3.140.22271440.191526652809100
3.14-3.45580.21851440.185626832827100
3.4558-3.95560.17991440.165226942838100
3.9556-4.98250.17331580.148227232881100
4.9825-43.59950.181570.182328643021100
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)
14.2931-1.09933.71892.4450.05647.63910.00030.02360.1258-0.2361-0.2185-0.0479-0.05240.07130.16440.147-0.0147-0.04370.10610.01910.2009-22.763242.3946-17.1402
21.648-0.00330.67461.6650.00913.1009-0.0266-0.21670.02970.22020.04240.0735-0.2969-0.05290.00730.23220.00150.01080.1673-0.00260.1601-22.924746.0222-13.265
32.0145-0.2564-1.13324.75640.2661.49680.0620.0349-0.21860.1781-0.01940.36140.2656-0.1172-0.04720.1691-0.0234-0.04480.16310.01180.2123-29.521330.7427-26.0595
41.0916-0.41220.24861.5288-0.33740.42920.0221-0.0327-0.0148-0.0401-0.0367-0.111-0.01540.02880.01540.15670.0039-0.0090.1994-0.0030.2061-9.417127.8962-25.288
52.5054-0.31640.17881.2344-0.30863.0228-0.1338-0.15290.08460.16230.0406-0.45820.07440.29540.08020.2127-0.0012-0.06570.1776-0.00590.3147-4.00737.4241-14.0987
63.45671.3802-0.06911.9212-0.11842.37810.3171-0.81750.30040.7709-0.286-0.0652-0.2159-0.1536-0.06870.4048-0.0046-0.02460.2684-0.06280.2379-8.86339.9659-4.8095
72.40690.7211.52753.42970.88124.0608-0.1180.08930.120.03960.0480.3438-0.089-0.32320.04630.129-0.0031-0.01640.1210.02290.1611-24.851110.8785-29.3864
82.81771.49910.23833.81310.93882.08270.20520.1039-0.3167-0.0329-0.0881-0.36730.1870.1895-0.10020.24390.057-0.0410.2530.0210.22812.8002-14.4809-16.8394
94.6266-1.3463.70851.87011.63287.948-0.14860.5830.4233-0.1768-0.2471-0.2127-0.31390.39570.30970.22750.0302-0.08180.24310.01670.25990.3404-13.2326-24.5954
100.49120.27630.56691.54350.47871.93950.0313-0.06640.00670.016-0.01950.09090.0387-0.069-0.0020.1524-0.01420.00940.17350.00690.1389-6.6805-4.935-13.6579
112.4340.82550.66072.67610.26491.709-0.0958-0.10140.27470.20770.0112-0.2386-0.22380.14880.08430.15510.0137-0.06590.15570.01180.1724-8.975315.9702-22.9723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 152 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 240 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 289 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 290 through 322 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 323 through 353 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 92 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 114 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 240 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 241 through 353 )B0

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