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- PDB-4yt5: HmdII from Methanocaldococcus jannaschii with bound methylene-tet... -

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Basic information

Entry
Database: PDB / ID: 4yt5
TitleHmdII from Methanocaldococcus jannaschii with bound methylene-tetrahydromethanopterin
ComponentsH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
KeywordsMETAL BINDING PROTEIN / Rossmann-like fold / [Fe]-hydrogenase paralog / 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 / HMD N-terminal domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / NAD(P)-binding Rossmann-like Domain ...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 / HMD N-terminal domain / 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
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN / TRIETHYLENE GLYCOL / H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)84,0875
Polymers82,3592
Non-polymers1,7283
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14920 Å2
ΔGint-129 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.000, 78.030, 153.920
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 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 10 - 353 / Label seq-ID: 10 - 353

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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


Mass: 41179.684 Da / Num. of mol.: 2 / Fragment: Rossmann-like domain, UNP residues 2-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1338 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58734
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-H4M / 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN


Mass: 788.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H45N6O16P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting 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: Aug 23, 2014
RadiationMonochromator: A Si(111) double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 50698 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 32.66 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 0.971 / Net I/σ(I): 18.81 / Num. measured all: 277687
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-20.8650.8362.9140229716770770.91798.7
2-2.10.9280.5364.5132478590658490.58999
2.1-2.40.9780.2478.46681012382122570.27299
2.4-2.70.9950.11615.341804752674780.12799.4
2.7-30.9970.06622.4625201482447790.07399.1
3-3.30.9990.04531.4318433325032310.04999.4
3.3-4.30.9990.02942.8828354544354050.03299.3
4.3-5.90.9990.02454.1915308281427950.02799.3
5.9-80.9980.02650.265196107910670.0398.9
8-120.9980.02757.5126965415230.0396.7
120.9980.02456.3211782562370.02792.6

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Processing

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

Resolution: 1.9→43.843 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 2535 5 %
Rwork0.1803 48159 -
obs0.1818 50694 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.86 Å2 / Biso mean: 42.5744 Å2 / Biso min: 16.72 Å2
Refinement stepCycle: final / Resolution: 1.9→43.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 118 183 5501
Biso mean--95.59 45.49 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095409
X-RAY DIFFRACTIONf_angle_d1.2137329
X-RAY DIFFRACTIONf_chiral_restr0.055875
X-RAY DIFFRACTIONf_plane_restr0.006925
X-RAY DIFFRACTIONf_dihedral_angle_d15.1142164
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2898X-RAY DIFFRACTION4TORSIONAL
12B2898X-RAY DIFFRACTION4TORSIONAL
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 (%)
1.9-1.93660.28141370.24572605274299
1.9366-1.97610.2881380.25282626276499
1.9761-2.0190.32321380.24332619275799
2.019-2.0660.27641400.22742665280599
2.066-2.11770.29631390.21362645278499
2.1177-2.17490.26771380.21292620275899
2.1749-2.23890.25171390.21052636277598
2.2389-2.31120.221400.20112663280399
2.3112-2.39380.24291400.19012661280199
2.3938-2.48960.25791390.19122643278299
2.4896-2.60290.24021420.18522685282799
2.6029-2.74010.23151410.187126762817100
2.7401-2.91180.20711400.18812676281699
2.9118-3.13650.20751430.184827052848100
3.1365-3.45210.21951410.17842682282399
3.4521-3.95130.17111440.158927422886100
3.9513-4.97710.17791450.1432743288899
4.9771-43.85450.17111510.17792867301898
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)
15.4216-0.7726-5.81244.18160.94167.46190.19310.0319-0.0627-0.2109-0.1569-0.0801-0.4570.09050.07680.20890.0572-0.02070.1875-0.01340.290923.0666-42.3938-17.1628
24.1109-1.3622-2.95933.45111.64432.2812-0.031-0.2849-0.00290.37180.1290.40380.1573-0.1147-0.03540.34870.00350.0650.26470.04610.217715.0972-43.6228-10.5796
32.70020.6627-0.89322.8857-0.71577.1204-0.0172-0.374-0.15330.31170-0.3690.42440.42210.09840.32910.0684-0.03720.2357-0.00830.268328.7-47.3991-15.2807
46.51780.3487-2.26618.95140.03633.1540.1403-0.46780.40411.08020.0258-0.4566-0.21280.4354-0.18280.3378-0.0022-0.03260.23170.0050.24229.844-32.9743-20.4058
52.7028-2.5738-0.03582.83531.61176.580.123-0.25540.36830.02240.0592-0.3751-0.30640.3147-0.32210.2603-0.04270.06080.2003-0.01390.28128.4006-34.0068-26.961
63.262-2.0482-0.83056.3353.9155.94720.20450.11550.4534-0.5430.0623-0.8944-0.58340.417-0.28020.263-0.02590.06390.2460.03120.319930.9878-26.4113-31.0781
73.0318-0.2172-2.07065.2062-2.32765.44270.04780.0715-0.09360.1155-0.01090.1833-0.0968-0.1319-0.00090.16760.008-0.03610.20350.00030.245314.8584-33.7188-26.9989
86.70160.59622.01022.00220.24353.6169-0.15810.04380.5649-0.0296-0.15820.4730.0133-0.41060.27860.2068-0.01350.05710.2148-0.06650.2882.5711-10.059-20.7186
95.4789-0.9154-1.73823.25520.35253.6842-0.0380.1363-0.57440.0065-0.03920.5980.0973-0.18680.04010.360.01790.02530.19520.010.30691.1477-7.7737-8.5179
105.98822.57580.4043.53310.38986.05240.5693-1.1286-0.24320.8989-0.4585-0.02960.15870.08-0.07320.42070.05950.01340.20690.0120.24069.1777-9.936-4.8828
114.2123-0.4065-1.45177.6985-2.42097.4143-0.03930.0456-0.1055-0.0109-0.0437-0.42640.16260.38740.08850.1857-0.04530.01080.1379-0.05820.174325.2519-10.9379-29.4096
124.94612.655-1.43023.663-0.78692.06840.15090.2520.253-0.1803-0.0280.2741-0.2103-0.3642-0.12710.32130.10240.0070.29480.01270.2298-7.971314.3956-18.7086
130.24320.1748-0.62962.0328-0.21711.69430.01840.00270.00630.0768-0.0442-0.0479-0.07880.004-0.0280.2284-0.0097-0.01010.25080.00110.22367.46273.274-12.5321
142.44261.1999-0.88413.5975-0.3262.1917-0.0742-0.0871-0.22660.2082-0.02630.2520.1733-0.16560.07110.21630.02480.03730.21-0.01970.2439.3884-16.0408-22.9791
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 52 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 92 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 114 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 130 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 152 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 215 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 262 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 263 through 289 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 290 through 322 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 323 through 353 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 10 through 130 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 131 through 240 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 241 through 353 )B0

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