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- PDB-4h16: Crystal Structure of a short chain alcohol dehydrogenase-related ... -

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Basic information

Entry
Database: PDB / ID: 4h16
TitleCrystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P6422
ComponentsShort chain alcohol dehydrogenase-related dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / NYSGRC / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


monocarboxylic acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / lipid metabolic process / oxidoreductase activity / metal ion 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
Short chain alcohol dehydrogenase-related dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGhosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P6422
Authors: Ghosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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_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.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.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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_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)28,1827
Polymers27,4871
Non-polymers6956
Water4,234235
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)112,72728
Polymers109,9464
Non-polymers2,78124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area20360 Å2
ΔGint-225 kcal/mol
Surface area35240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.2, 129.2, 103.5
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -x,-y-1,z; x,x-y-1,-z-1/3 and -x,-x+y,-z-1/3

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Components

#1: Protein Short chain alcohol dehydrogenase-related dehydrogenase


Mass: 27486.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0888, SMa1629 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL
References: UniProt: Q92YJ2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 4.54 Å3/Da / Density % sol: 72.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium Chloride 0.1 M HEPES:NaOH pH 7.5, and 30% (v/v) PPG P400, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65029 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.414 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.034.50.88432591.4071100
2.03-2.074.50.74432911.3931100
2.07-2.114.60.61732391.5031100
2.11-2.154.60.57332651.461100
2.15-2.24.60.4732521.491100
2.2-2.254.60.37432461.5721100
2.25-2.314.70.34632891.5691100
2.31-2.374.70.332331.6031100
2.37-2.444.70.27332981.6441100
2.44-2.524.70.22132541.6231100
2.52-2.614.70.20432501.5351100
2.61-2.714.70.16932871.4881100
2.71-2.844.70.1532411.4841100
2.84-2.994.70.12932611.421100
2.99-3.174.70.1132641.309199.9
3.17-3.424.70.132671.294199.8
3.42-3.764.70.08732341.179199
3.76-4.314.60.07432201.028198.4
4.31-5.434.50.0631871.096197.4
5.43-504.70.03831921.139197.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Code:

Resolution: 2→37.294 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.19 / σ(F): 1.91 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 3266 5.03 %RANDOM
Rwork0.1629 ---
obs0.1636 64983 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.62 Å2 / Biso mean: 30.2639 Å2 / Biso min: 7.4 Å2
Refinement stepCycle: LAST / Resolution: 2→37.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 42 235 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081999
X-RAY DIFFRACTIONf_angle_d1.0782706
X-RAY DIFFRACTIONf_chiral_restr0.068319
X-RAY DIFFRACTIONf_plane_restr0.005349
X-RAY DIFFRACTIONf_dihedral_angle_d17.923764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0005-2.03030.32881370.280926822819100
2.0303-2.0620.29811450.259526942839100
2.062-2.09580.26411350.224927102845100
2.0958-2.1320.23471360.214726622798100
2.132-2.17070.21031500.209427092859100
2.1707-2.21250.18261400.196826922832100
2.2125-2.25760.24131490.227072856100
2.2576-2.30670.2021450.183227152860100
2.3067-2.36040.22621490.167326572806100
2.3604-2.41940.21241210.168927152836100
2.4194-2.48480.17031460.164227012847100
2.4848-2.55790.21370.1626702807100
2.5579-2.64040.23681420.155827122854100
2.6404-2.73480.16191310.145426962827100
2.7348-2.84420.17911650.148226792844100
2.8442-2.97360.1851380.147526932831100
2.9736-3.13030.15571510.150927092860100
3.1303-3.32630.17811420.143626662808100
3.3263-3.5830.13871480.14122680282899
3.583-3.94320.12521630.12432662282599
3.9432-4.51290.1621380.13282612275097
4.5129-5.68260.16371360.15542653278998
5.6826-37.30070.19731220.21152641276397
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)
13.12610.478-0.09321.031-0.38621.19020.0037-0.81140.18960.3295-0.1517-0.0608-0.12170.10250.09650.0939-0.0242-0.04910.5089-0.04640.145650.3343-45.25398.2559
21.3172-0.0440.09111.329-0.00471.2102-0.0541-0.3238-0.01120.0129-0.0444-0.1074-0.12990.27290.09490.06220.0154-0.0160.17480.01010.140747.0381-46.9968-9.6889
32.7346-0.06740.05530.63410.05873.3904-0.0372-0.60780.8028-0.0013-0.1708-0.0765-1.12970.0111-0.03450.06940.0634-0.05940.1999-0.15290.33531.9001-42.0778-2.7225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 82 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 172 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 259 )A0

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