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- PDB-3ged: Fingerprint and Structural Analysis of a Apo SCOR enzyme from Clo... -

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Basic information

Entry
Database: PDB / ID: 3ged
TitleFingerprint and Structural Analysis of a Apo SCOR enzyme from Clostridium thermocellum
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / sdr / SCOR / Rossmann Fold
Function / homology
Function and homology information


steroid metabolic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOSULFATE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesClostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.698 Å
AuthorsHuether, R. / Liu, Z.J. / Xu, H. / Wang, B.C. / Pletnev, V. / Mao, Q. / Umland, T. / Duax, W.
CitationJournal: Proteins / Year: 2010
Title: Sequence fingerprint and structural analysis of the SCOR enzyme A3DFK9 from Clostridium thermocellum.
Authors: Huether, R. / Liu, Z.J. / Xu, H. / Wang, B.C. / Pletnev, V.Z. / Mao, Q. / Duax, W.L. / Umland, T.C.
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMar 17, 2009ID: 3DII
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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

Downloads & links

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4269
Polymers54,8592
Non-polymers5677
Water9,926551
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,85118
Polymers109,7184
Non-polymers1,13314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area22240 Å2
ΔGint-193 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.287, 124.287, 162.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-416-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 27429.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum ATCC 27405 (bacteria)
Strain: strain ATCC 27405 / DSM 1237 / Gene: Cthe_1510 / Plasmid: pETSumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A3DFK9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-THJ / THIOSULFATE / Thiosulfate


Mass: 112.128 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O3S2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 298 K
Details: 25% (w/v) PEG 4000,100mM TAPs pH 9.0, 50mM sodium thiosulfate pentahydrate 1:1 cocktail to protein ratio (10mg/ml), hanging drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979454 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 1.416→99.015 Å / Num. obs: 68407 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.9
Reflection shellResolution: 1.69→1.74 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1YDE, 1VL8

1yde

1vl8


Resolution: 1.698→49.684 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 3442 5.03 %
Rwork0.179 --
obs0.18 68407 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.211 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 94.99 Å2 / Biso mean: 32.972 Å2 / Biso min: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.339 Å20 Å20 Å2
2---0.339 Å2-0 Å2
3---0.677 Å2
Refinement stepCycle: LAST / Resolution: 1.698→49.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 29 551 4338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113866
X-RAY DIFFRACTIONf_angle_d1.3275220
X-RAY DIFFRACTIONf_chiral_restr0.094577
X-RAY DIFFRACTIONf_plane_restr0.007669
X-RAY DIFFRACTIONf_dihedral_angle_d15.8481398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.698-1.7220.2331490.2152528267796
1.722-1.7460.2371300.2022594272499
1.746-1.7720.2551310.20226202751100
1.772-1.80.2211360.19426242760100
1.8-1.8290.2341570.18426062763100
1.829-1.8610.2051450.1772581272699
1.861-1.8950.2591260.2112442256892
1.895-1.9310.4691180.3852331244988
1.931-1.9710.2571570.2112437259494
1.971-2.0140.1951370.1652594273199
2.014-2.060.2131560.162621277799
2.06-2.1120.191180.1622636275499
2.112-2.1690.1831380.1652603274199
2.169-2.2330.2421300.1922502263295
2.233-2.3050.2591230.2352475259893
2.305-2.3870.2081540.1742621277599
2.387-2.4830.171480.1612625277399
2.483-2.5960.21190.1722676279599
2.596-2.7330.2111280.172643277199
2.733-2.9040.2181300.18326672797100
2.904-3.1280.2081570.18126642821100
3.128-3.4430.1671450.15526752820100
3.443-3.9410.1761290.1452681281099
3.941-4.9640.1791330.1442721285499
4.964-49.7050.2091480.1982798294698
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)
10.4478-0.33050.08170.8333-0.06410.7688-0.1066-0.30440.0930.08140.11760.0295-0.1747-0.045-0.0335-0.0411-0.0143-0.01790.1118-0.06110.04255.303774.912158.4871
20.6577-0.3-0.00490.59220.02840.5350.07510.0234-0.0253-0.2787-0.05850.1233-0.0186-0.159-0.050.0729-0.0664-0.065-0.0408-0.01610.032249.319869.064929.4268
32.2364-2.012.22358.0644-4.54542.29360.0862-0.9287-1.5289-0.1307-0.17111.3606-1.5452-2.57110.0920.15710.094-0.0260.3149-0.12520.29768.275180.242453.9859
42-5.3825-6.23942220.59292.23662.3133-4.43292.24970.2337-6.0343-9.9705-2.84240.580.1468-0.05880.37150.00510.395244.156155.956433.9526
522.8052222-0.0933-0.49423.581-7.22150.49627.8391-3.518610.7451-0.41020.61940.0096-0.08990.6651-0.01420.538459.030978.393365.9691
62-6.10054.000120.886320.3274-8.67126.8588-1.17650.48951.80329.4416-2.2757-0.83310.65810.00880.03320.7298-0.09790.596345.709365.118821.9721
727.279822-7.68222-0.3074-0.04532.6135-0.11141.28067.68830.80645.5806-0.96420.12830.0775-0.03110.3314-0.07410.507450.693893.368764.6308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G

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