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- PDB-3r1i: Crystal structure of a short-chain type dehydrogenase/reductase f... -

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Basic information

Entry
Database: PDB / ID: 3r1i
TitleCrystal structure of a short-chain type dehydrogenase/reductase from Mycobacterium marinum
ComponentsShort-chain type dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / tuberculosis / water contaminant / water borne pathogen / dehydrogenase / NAD / NADP / SDR
Function / homology
Function and homology information


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 type dehydrogenase/reductase
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 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_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.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_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 type dehydrogenase/reductase
B: Short-chain type dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3255
Polymers58,2152
Non-polymers1113
Water6,485360
1
A: Short-chain type dehydrogenase/reductase
B: Short-chain type dehydrogenase/reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)116,65010
Polymers116,4294
Non-polymers2216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area15790 Å2
ΔGint-184 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.520, 127.910, 105.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-256-

MG

21B-256-

MG

31A-259-

HOH

41B-261-

HOH

51B-263-

HOH

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Components

#1: Protein Short-chain type dehydrogenase/reductase


Mass: 29107.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: MMAR_2849 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HE09
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MymaA.01365.b.A1 PS00949 at 55 mg/mL against JCSF+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: MymaA.01365.b.A1 PS00949 at 55 mg/mL against JCSF+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220110d6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 10, 2011 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 42084 / Num. obs: 41849 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 27.831 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.95-23.20.433.1498773084306599.4
2-2.060.3583.849937297799.6
2.06-2.120.2825.1510194292699.7
2.12-2.180.2296.8611464281699.7
2.18-2.250.1879.0912271274399.2
2.25-2.330.15910.7412340262798.7
2.33-2.420.13612.0712576255499.6
2.42-2.520.11913.9312744245999.5
2.52-2.630.10715.5413033236899.3
2.63-2.760.09618.0113406225399.6
2.76-2.910.08521.1114968217199.4
2.91-3.080.06725.6914885203599.1
3.08-3.30.05929.4314154192999.5
3.3-3.560.04635.6413245181299.7
3.56-3.90.03942.3212108165599.6
3.9-4.360.03447.5210957150899.3
4.36-5.030.03251.99868136399.6
5.03-6.170.03148.0383051148100
6.17-8.720.02751.58646491199.8
8.720.02458.49344452997.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.24 Å
Translation2.5 Å39.24 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ctm

3ctm


Resolution: 1.95→39.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1712 / WRfactor Rwork: 0.1452 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8729 / SU B: 6.264 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1352 / SU Rfree: 0.1252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2105 5 %RANDOM
Rwork0.1637 ---
obs0.1655 41760 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.42 Å2 / Biso mean: 21.951 Å2 / Biso min: 7.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--1.38 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 6 360 4011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223741
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.975097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17724.453137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42315599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8361520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212790
X-RAY DIFFRACTIONr_mcbond_it0.6751.52490
X-RAY DIFFRACTIONr_mcangle_it1.17923986
X-RAY DIFFRACTIONr_scbond_it2.00131251
X-RAY DIFFRACTIONr_scangle_it3.3234.51106
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 151 -
Rwork0.207 2902 -
all-3053 -
obs--99.19 %
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)
10.4509-0.1363-0.05710.3645-0.10160.61080.0080.097-0.0762-0.0492-0.02380.00390.0397-0.11630.01580.04360.008-0.01850.0498-0.03010.032832.566316.12598.1071
20.4485-0.017-0.10810.0239-0.06620.8888-0.0168-0.0232-0.02340.01460.0006-0.0152-0.0544-0.14940.01620.01760.0063-0.00120.053-0.01040.042922.974221.444335.0741
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 255
2X-RAY DIFFRACTION2B1 - 255

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