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- PDB-3geg: Fingerprint and Structural Analysis of a SCOR enzyme with its bou... -

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Basic information

Entry
Database: PDB / ID: 3geg
TitleFingerprint and Structural Analysis of a SCOR enzyme with its bound cofactor 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THIOSULFATE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesClostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 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: 3DIJ
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)56,5289
Polymers54,8592
Non-polymers1,6697
Water5,278293
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)113,05618
Polymers109,7184
Non-polymers3,33814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area26090 Å2
ΔGint-213 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.272, 124.272, 161.208
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
11A-378-

HOH

21A-384-

HOH

31B-369-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 300 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: 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
#4: Chemical ChemComp-THJ / THIOSULFATE / Thiosulfate


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion
Details: 25% (w/v) PEG 4000,100mM TAPs pH9.0, 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: 2.1→50 Å / Num. obs: 36901 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GED

3ged


Resolution: 2.102→43.937 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1841 4.99 %
Rwork0.167 --
obs0.169 36874 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.103 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 96.27 Å2 / Biso mean: 30.321 Å2 / Biso min: 4.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.836 Å2-0 Å20 Å2
2---0.836 Å20 Å2
3---1.636 Å2
Refinement stepCycle: LAST / Resolution: 2.102→43.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 107 293 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013946
X-RAY DIFFRACTIONf_angle_d1.335345
X-RAY DIFFRACTIONf_chiral_restr0.507591
X-RAY DIFFRACTIONf_plane_restr0.004675
X-RAY DIFFRACTIONf_dihedral_angle_d17.7541519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.102-2.1580.231530.18626302783100
2.158-2.2220.2281220.18626932815100
2.222-2.2940.241400.17126712811100
2.294-2.3760.2021460.16326572803100
2.376-2.4710.211450.15726582803100
2.471-2.5830.21310.16426752806100
2.583-2.7190.2311330.1726962829100
2.719-2.890.221690.18226662835100
2.89-3.1130.231370.18126912828100
3.113-3.4260.1741330.16727172850100
3.426-3.9210.1641400.14727162856100
3.921-4.9390.1681450.1427562901100
4.939-43.9460.1971470.1852807295497
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)
10.2705-0.2815-0.1230.84850.080.5321-0.0602-0.30830.11110.08930.06180.0918-0.1021-0.04610.00380.0293-0.02040.00120.2227-0.07060.075655.274274.894958.257
20.5581-0.32020.06880.7614-0.17740.42450.0433-0.01930.0144-0.3335-0.05220.12730.0247-0.0744-0.04170.1372-0.0311-0.07050.0289-0.0180.041949.376269.017329.2747
30.63690.34490.10490.1259-0.0828-0.0684-0.0705-0.15820.0147-0.0132-0.0484-0.00170.0769-0.18680.04970.5701-0.24860.04810.7146-0.10570.47759.391279.195962.083
4-0.0586-0.1470.0177-0.62440.11570.1176-0.0297-0.0023-0.0123-0.2073-0.0742-0.0124-0.07010.0160.05070.9135-0.225-0.32190.62390.08050.544845.149464.863525.4017
52-4.44427.14727.2778.41229.45190.1107-0.447-0.11530.5654-0.0357-1.53410.13390.2791-0.08540.3712-0.0685-0.020.5458-0.11730.415368.13879.045353.5755
62.13525.82112.30892.16524.87462.17790.05920.2545-1.50790.3336-0.0015-1.3410.12110.0075-0.06770.384-0.0789-0.00380.3262-0.06140.619545.365956.205434.0075
725.510722-9.15192-0.89811.18051.6046-0.38540.58114.42180.9332.83510.32420.20480.02190.04670.2852-0.18380.808950.625193.307764.282
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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