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- PDB-4j2h: Crystal structure of a putative short-chain alcohol dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 4j2h
TitleCrystal structure of a putative short-chain alcohol dehydrogenase from Sinorhizobium meliloti 1021 (Target NYSGRC-011708)
ComponentsShort chain alcohol dehydrogenase-related dehydrogenase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium / dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
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
Short chain alcohol dehydrogenase-related dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. ...Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative short-chain alcohol dehydrogenase from Sinorhizobium meliloti 1021 (Target NYSGRC-011708)
Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Short chain alcohol dehydrogenase-related dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6208
Polymers27,0491
Non-polymers5727
Water1,18966
1
A: Short chain alcohol dehydrogenase-related dehydrogenase
hetero molecules

A: Short chain alcohol dehydrogenase-related dehydrogenase
hetero molecules

A: Short chain alcohol dehydrogenase-related dehydrogenase
hetero molecules

A: Short chain alcohol dehydrogenase-related dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,48232
Polymers108,1954
Non-polymers2,28628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area19420 Å2
ΔGint-101 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.875, 103.875, 101.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Short chain alcohol dehydrogenase-related dehydrogenase


Mass: 27048.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0207, SMa0389 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q930I9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG4 #82; G10: 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 20% (v/v) 2-Propanol); Cryoprotection (30% Ethylene glycol), ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG4 #82; G10: 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 20% (v/v) 2-Propanol); Cryoprotection (30% Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19305 / Num. obs: 19305 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 41.7 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.075 / Net I/σ(I): 41.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 42.9 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 939 / Rsym value: 0.998 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→36.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.216 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 980 5.1 %RANDOM
Rwork0.1889 ---
obs0.1902 19172 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.18 Å2 / Biso mean: 61.0321 Å2 / Biso min: 33.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 34 66 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191909
X-RAY DIFFRACTIONr_bond_other_d0.0010.021843
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9592579
X-RAY DIFFRACTIONr_angle_other_deg0.77134205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41822.94978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.061517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 71 -
Rwork0.265 1312 -
all-1383 -
obs--99.86 %
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)
11.50750.21880.1131.32-0.08982.90530.0807-0.2815-0.12170.3554-0.23090.35850.2658-0.80850.15020.4271-0.12920.08020.3042-0.08710.316437.4734-3.919214.9271
2125.901-47.8992-67.08124.496832.559743.6402-0.6209-0.75540.32820.3820.7307-0.0830.49310.8885-0.10980.21960.0670.05380.18610.01410.258740.6839-16.79463.2274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 255
2X-RAY DIFFRACTION2A307

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