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- PDB-3rf7: Crystal structure of an Iron-containing alcohol dehydrogenase (Sd... -

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Basic information

Entry
Database: PDB / ID: 3rf7
TitleCrystal structure of an Iron-containing alcohol dehydrogenase (Sden_2133) from Shewanella denitrificans OS-217 at 2.12 A resolution
ComponentsIron-containing alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Unknown ligand / Iron-containing alcohol dehydrogenase
Similarity search - Component
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an Iron-containing alcohol dehydrogenase (Sden_2133) from Shewanella denitrificans OS-217 at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,08014
Polymers42,6301
Non-polymers1,45013
Water6,431357
1
A: Iron-containing alcohol dehydrogenase
hetero molecules

A: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,16128
Polymers85,2602
Non-polymers2,90126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area8500 Å2
ΔGint-184 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.074, 121.074, 275.666
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-596-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Iron-containing alcohol dehydrogenase


Mass: 42629.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans (bacteria) / Strain: OS217 / ATCC BAA-1090 / DSM 15013 / Gene: Sden_2133 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q12MB1

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Non-polymers , 9 types, 370 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.300M calcium chloride, 26.00% polyethylene glycol 400, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.12→29.947 Å / Num. all: 58332 / Num. obs: 58332 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 33.086 Å2 / Rsym value: 0.166 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.12-2.187.51.3881.63149542261.388100
2.18-2.237.51.07923104741571.079100
2.23-2.37.50.8592.43015440470.859100
2.3-2.377.50.7292.82929239250.729100
2.37-2.457.50.6043.22848438140.604100
2.45-2.537.50.47342748236780.473100
2.53-2.637.50.4184.52673635750.418100
2.63-2.747.50.3285.42552634150.328100
2.74-2.867.40.2596.52458633010.259100
2.86-37.50.2097.92362731600.209100
3-3.167.50.1679.62245330130.167100
3.16-3.357.50.13611.52137228670.136100
3.35-3.587.40.11413.81990326820.114100
3.58-3.877.40.09816.61875525280.098100
3.87-4.247.40.0918.21708623120.09100
4.24-4.747.30.07920.11554421180.079100
4.74-5.477.30.08119.31375318860.081100
5.47-6.77.20.09417.61161416150.094100
6.7-9.4870.08119.8897112800.081100
9.48-29.9476.40.06620.746937330.06697

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.12→29.947 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 5.271 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD (MOTION DETERMINATION) SERVER. 6. CALCIUM AND CHLORIDE IONS, AND HEPES (EPE) MOLECULES FROM THE CRYSTALLIZATION ARE MODELED INTO THE STRUCTURE. 7. X-RAY ANOMALOUS SCATTERING MEASUREMENTS INDICATE A MIXTURE OF AN IRON (FE) AND A NICKEL (NI) ATOM IS WITHIN COORDINATION DISTANCE OF THE SIDE CHAINS OF ASP-194, HIS-198, HIS-258, AND HIS-272. THE OCCUPANCIES OF THE METAL IONS WERE ESTIMATED FROM THE RATIOS OF THEIR ANOMALOUS DIFFERENCE MAP PEAK HEIGHTS AT WAVELENGTHS ABOVE AND BELOW THE FE AND NI K-SHELL ABSORPTION EDGES. REDUCING THE TOTAL OCCUPANCY OF THE FE/NI SITE TO 0.8 RESULTED IN BETTER AGREEMENT BETWEEN THE B-FACTORS OF THE METAL ATOMS AND ATOMS ON THE PROTEIN WITHIN COORDINATION DISTANCE. 8. ADDITIONAL ELECTRON DENSITY AT THE PUTATIVE ACTIVE SITE WAS MODELED AS AN UNKNOWN LIGAND (UNL). THE UNL COULD REPRESENT AN ANALOG TO THE SUBSTITUTED NADP THAT WAS IDENTIFIED IN THE E.COLI ALCOHOL DEHYDROGENASE YQHD (1OJ7) STRUCTURE. HOWEVER, MODELING IT AS AN NC5 AND NC6 SUBSTITUTED NAD RESULTED IN RESIDUAL DIFFERENCE DENSITY AT THE SITE SUGGESTING THAT EITHER THIS WAS NOT FULLY OCCUPIED AND WAS A MIXTURE OF COMPOUNDS OR IT WAS NOT THE CORRECT ANALOG. WITHOUT ADDITIONAL DATA TO IDENTIFY THE COMPOUND(S), WE HAVE CHOSEN TO MODEL IT AS A UNL ADJACENT TO THE NAD AND METAL SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 2951 5.1 %RANDOM
Rwork0.1819 ---
obs0.1826 58283 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.81 Å2 / Biso mean: 38.9231 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--1.28 Å20 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 83 357 3227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223019
X-RAY DIFFRACTIONr_bond_other_d0.0010.021980
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9814112
X-RAY DIFFRACTIONr_angle_other_deg0.90934870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6235381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18525.116129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58115493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.458159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213375
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02579
X-RAY DIFFRACTIONr_mcbond_it0.6991.51853
X-RAY DIFFRACTIONr_mcbond_other0.1351.5756
X-RAY DIFFRACTIONr_mcangle_it1.33223002
X-RAY DIFFRACTIONr_scbond_it2.09131166
X-RAY DIFFRACTIONr_scangle_it3.1034.51109
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 195 -
Rwork0.319 4021 -
all-4216 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 71.2795 Å / Origin y: 13.3079 Å / Origin z: 42.6717 Å
111213212223313233
T0.1514 Å20.017 Å2-0.0054 Å2-0.0175 Å20.0176 Å2--0.0499 Å2
L0.143 °20.0649 °2-0.0845 °2-0.3956 °2-0.0279 °2--0.5854 °2
S-0.0456 Å °-0.0469 Å °-0.0254 Å °-0.1145 Å °-0.0303 Å °-0.0546 Å °-0.0821 Å °0.0413 Å °0.0759 Å °

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