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- PDB-2gvi: Crystal structure of a putative formylmethanofuran dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 2gvi
TitleCrystal structure of a putative formylmethanofuran dehydrogenase subunit e (ta1109) from thermoplasma acidophilum at 1.87 A resolution
Componentsconserved hypothetical protein
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


GTP binding / metal ion binding
Similarity search - Function
pa2218 like fold / pa2218 like domain / Pa2218-like domain superfamily / Formylmethanofuran dehydrogenase, subunit E domain / FmdE, Molybdenum formylmethanofuran dehydrogenase operon / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Tubulin/FtsZ, C-terminal domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ-like, C-terminal domain ...pa2218 like fold / pa2218 like domain / Pa2218-like domain superfamily / Formylmethanofuran dehydrogenase, subunit E domain / FmdE, Molybdenum formylmethanofuran dehydrogenase operon / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Tubulin/FtsZ, C-terminal domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ-like, C-terminal domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Unknown ligand / : / FmdE domain-containing protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / MAD, molecular replacement / Resolution: 1.87 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
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG: MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG: MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,63221
Polymers23,4521
Non-polymers1,18020
Water2,324129
1
A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,26342
Polymers46,9042
Non-polymers2,36040
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area9850 Å2
ΔGint-258 kcal/mol
Surface area17700 Å2
MethodPISA
2
A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,52784
Polymers93,8074
Non-polymers4,71980
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)78.680, 97.650, 75.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein conserved hypothetical protein


Mass: 23451.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: 10640422 / Production host: Escherichia coli (E. coli) / References: GenBank: 10640422, UniProt: Q9HJ63*PLUS

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Non-polymers , 5 types, 149 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.8756.79DATA FROM A MONOCLINIC C2 CRYSTAL FORM CONTAINING SE-MET WAS USED FOR THE MAD PHASING EXPERIMENTS AND DETERMINATION OF THE STRUCTURE AT A RESOLUTION OF 2.0 ANGSTROMS. THIS 2.0 ANGSTROM MAD STRUCTURE WAS USED AS A MOLECULAR REPLACEMENT MODEL TO DETERMINE THE STRUCTURE AT AN ENHANCED RESOLUTION OF 1.87 ANGSTROMS IN THE I222 SPACEGROUP.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop610.0% PEG-8000, 0.2M Zn(OAc)2, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop60.2M MgNO3, 20.0% PEG-3350, No Buffer pH 5.8, pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.000001
SYNCHROTRONSSRL BL9-220.97918, 0.91837, 0.97903
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 19, 2006Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDMar 12, 2006Flat collimating mirror, toroid focusing mirror
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2Double crystal monochromator
Radiation wavelength
IDWavelength (Å)Relative weight
11.0000011
20.979181
30.918371
40.979031
ReflectionResolution: 1.87→30.08 Å / Num. obs: 24246 / % possible obs: 99.5 % / Redundancy: 4.05 % / Biso Wilson estimate: 28.07 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.38
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.87-1.9499.50.6981.2794611,299.5
1.94-2.0199.70.5281.6783461,2
2.01-2.1199.50.4012.23100161,2
2.11-2.2299.70.2793.1291641,2
2.22-2.3699.80.223.9293191,2
2.36-2.5499.60.1615.1891071,2
2.54-2.7999.80.1186.9492121,2
2.79-3.1999.60.07510.0292831,2
3.19-4.0299.10.0416.8693491,2
4.02-30.198.40.02425.7894411,2

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Phasing

PhasingMethod: MAD, molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
PHASERphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.87→30.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.854 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3). GLYCEROL, ACETATE, AND ZINC CATIONS ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS. 4). X-RAY ANOMALOUS SCATTERING MEASUREMENTS INDICATE ZINC CATIONS ARE COORDINATED TO HIS AND CYS SIDECHAIN ATOMS. 5). ATOM RECORD CONTAINS RESIDUAL B FACTORS 6). ELECTRON DENSITY INDICATED THAT THE SIDECHAIN SULFUR ATOM OF OF CYS 61 NEAR THE PUTATIVE ACTIVE SITE IS IN COVALENT BONDING DISTANCE OF AN UNKNOWN MOLECULE, AND AN UNKNOWN LIGAND (UNL) WAS MODELED AT THIS POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1229 5.1 %RANDOM
Rwork0.19 ---
all0.191 ---
obs0.19109 24246 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.87→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 68 129 1779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221710
X-RAY DIFFRACTIONr_bond_other_d0.0030.021533
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9892279
X-RAY DIFFRACTIONr_angle_other_deg1.13133553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6095207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.19723.11777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.22515272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8741511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021906
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02367
X-RAY DIFFRACTIONr_nbd_refined0.1790.3298
X-RAY DIFFRACTIONr_nbd_other0.1250.31452
X-RAY DIFFRACTIONr_nbtor_refined0.1770.5804
X-RAY DIFFRACTIONr_nbtor_other0.0810.5886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5165
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.338
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1410.3111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.543
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.090.51
X-RAY DIFFRACTIONr_mcbond_it1.5331075
X-RAY DIFFRACTIONr_mcbond_other0.3283419
X-RAY DIFFRACTIONr_mcangle_it2.32351627
X-RAY DIFFRACTIONr_scbond_it3.8618753
X-RAY DIFFRACTIONr_scangle_it5.00311649
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 77 -
Rwork0.279 1671 -
obs-1748 99.77 %
Refinement TLS params.Method: refined / Origin x: 33.842 Å / Origin y: 19.94 Å / Origin z: 4.083 Å
111213212223313233
T-0.1532 Å20.0103 Å2-0.0024 Å2--0.1698 Å2-0.0107 Å2---0.1275 Å2
L1.5761 °2-0.5123 °2-0.5528 °2-0.5735 °20.1213 °2--0.7577 °2
S-0.0546 Å °-0.0905 Å °0.1003 Å °0.0103 Å °0.0476 Å °-0.0118 Å °-0.101 Å °-0.0208 Å °0.007 Å °
Refinement TLS groupSelection: ALL

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