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- PDB-3d00: Crystal structure of a tungsten formylmethanofuran dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3d00
TitleCrystal structure of a tungsten formylmethanofuran dehydrogenase subunit e (fmde)-like protein (syn_00638) from syntrophus aciditrophicus at 1.90 A resolution
ComponentsTungsten formylmethanofuran dehydrogenase subunit E
KeywordsMETAL BINDING PROTEIN / Fwde/gapdh domain-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


60s Ribosomal Protein L30; Chain: A; - #130 / Formylmethanofuran dehydrogenase, subunit E domain / FmdE, Molybdenum formylmethanofuran dehydrogenase operon / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tungsten formylmethanofuran dehydrogenase subunit E
Similarity search - Component
Biological speciesSyntrophus aciditrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved alpha+beta core domain and an auxiliary C-terminal treble-clef zinc finger.
Authors: Axelrod, H.L. / Das, D. / Abdubek, P. / Astakhova, T. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. ...Authors: Axelrod, H.L. / Das, D. / Abdubek, P. / Astakhova, T. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Lam, W.W. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tungsten formylmethanofuran dehydrogenase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7983
Polymers21,6981
Non-polymers1012
Water75742
1
A: Tungsten formylmethanofuran dehydrogenase subunit E
hetero molecules

A: Tungsten formylmethanofuran dehydrogenase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5976
Polymers43,3952
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4350 Å2
ΔGint-59 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.356, 54.356, 136.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein Tungsten formylmethanofuran dehydrogenase subunit E


Mass: 21697.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophus aciditrophicus (bacteria) / Strain: SB / Gene: YP_460196.1, SYNAS_01490, SYN_00638 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2LQ23
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01M NiCl2, 20.0% PEG MME 2000, 0.1M Tris-HCl pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97817
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978171
ReflectionResolution: 1.9→29.386 Å / Num. obs: 16955 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 30.675 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 6.8
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.957.10.7862612081.13499.9
1.95-27.20.9858211920.85599.9
2-2.067.11.2825311570.659100
2.06-2.127.11.6802011220.484100
2.12-2.197.21.9788711020.41100
2.19-2.277.12.3754910680.34100
2.27-2.367.22.8732510180.281100
2.36-2.457.13.370329890.235100
2.45-2.567.14.267439530.185100
2.56-2.697.15.165229200.148100
2.69-2.8376.161428720.122100
2.83-377.358348370.097100
3-3.2178.655697960.079100
3.21-3.47710.550247180.062100
3.47-3.86.913.247486930.049100
3.8-4.256.813.642726310.044100
4.25-4.916.714.837485610.041100
4.91-6.016.51631734850.041100
6.01-8.5614.323533940.041100
8.5-29.3865.216.412442390.03595.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.386 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.433 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.156
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ZINC WAS MODELED BASED ON X-RAY FLUORESCENCE SCAN AND ANOMALOUS DIFFERENCE FOURIER MAP CALCULATIONS. 5. CHLORIDE WAS MODELED BASED ON CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 855 5.1 %RANDOM
Rwork0.233 ---
obs0.235 16902 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2--1.73 Å20 Å2
3----3.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 2 42 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221445
X-RAY DIFFRACTIONr_bond_other_d0.0030.02961
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9871972
X-RAY DIFFRACTIONr_angle_other_deg1.03132356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47423.77453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66115225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.608156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
X-RAY DIFFRACTIONr_nbd_refined0.20.2285
X-RAY DIFFRACTIONr_nbd_other0.1960.2900
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2710
X-RAY DIFFRACTIONr_nbtor_other0.0870.2747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.215
X-RAY DIFFRACTIONr_mcbond_it1.2142954
X-RAY DIFFRACTIONr_mcbond_other0.2642376
X-RAY DIFFRACTIONr_mcangle_it1.91331489
X-RAY DIFFRACTIONr_scbond_it1.0862576
X-RAY DIFFRACTIONr_scangle_it1.5763480
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 64 -
Rwork0.347 1136 -
all-1200 -
obs--99.75 %
Refinement TLS params.Method: refined / Origin x: 16.6441 Å / Origin y: 25.3781 Å / Origin z: 61.974 Å
111213212223313233
T-0.1523 Å2-0.0519 Å20.0003 Å2--0.1421 Å20.0085 Å2---0.1545 Å2
L1.5378 °2-1.5082 °22.3567 °2-3.3908 °2-3.3548 °2--5.9005 °2
S-0.0174 Å °0.2052 Å °0.1697 Å °0.1243 Å °-0.1391 Å °-0.1022 Å °-0.3315 Å °0.008 Å °0.1565 Å °

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