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- PDB-3rih: Crystal structure of a putative short chain dehydrogenase or redu... -

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Basic information

Entry
Database: PDB / ID: 3rih
TitleCrystal structure of a putative short chain dehydrogenase or reductase from Mycobacterium abscessus
Componentsshort chain dehydrogenase or reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tuberculosis / water contaminant / putative uncharacterized protein / potassium ion
Function / homology
Function and homology information


fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
PKS_KR / 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
: / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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
DepositionApr 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 dehydrogenase or reductase
B: short chain dehydrogenase or reductase
C: short chain dehydrogenase or reductase
D: short chain dehydrogenase or reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,18531
Polymers120,1364
Non-polymers2,04927
Water14,826823
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22420 Å2
ΔGint-30 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.550, 208.550, 94.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
short chain dehydrogenase or reductase


Mass: 30034.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_0952 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MJ88
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / 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: 4.28 Å3/Da / Density % sol: 71.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MyabA.01365.a.A1 PS00935 at 68.8 mg/mL against JCSG+ B12: 0.2 M potassium citrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 219942b12, pH 7.5, VAPOR ...Details: MyabA.01365.a.A1 PS00935 at 68.8 mg/mL against JCSG+ B12: 0.2 M potassium citrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 219942b12, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 113114 / Num. obs: 113051 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 28.642 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 16.32
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
2.15-2.218.20.5434.04672068232823299.9
2.21-2.270.4995.172158804899.8
2.27-2.330.4715.2273407782099.8
2.33-2.40.3666.6673746762699.9
2.4-2.480.3067.88733627394100
2.48-2.570.2768.88728747147100
2.57-2.670.24110.15727026913100
2.67-2.780.21811.3721886671100
2.78-2.90.17813.62716636405100
2.9-3.040.15515.66701066128100
3.04-3.210.12718.75678505841100
3.21-3.40.10522.44646535548100
3.4-3.630.08826.87609585214100
3.63-3.930.07630.66565114868100
3.93-4.30.06134.9953249449299.9
4.3-4.810.05536.95484114088100
4.81-5.550.05435.91426233638100
5.55-6.80.05632.68362173105100
6.8-9.620.03741.91289772444100
9.620.0343.8715756142999

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.36 Å
Translation3 Å49.36 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PK0

3pk0


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1613 / WRfactor Rwork: 0.1413 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9065 / SU B: 5.669 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1134 / SU Rfree: 0.1087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 5653 5 %RANDOM
Rwork0.1543 ---
obs0.1555 112763 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.62 Å2 / Biso mean: 22.2602 Å2 / Biso min: 6.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7314 0 128 823 8265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227589
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.98610321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41551055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64723.79248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.952151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6471549
X-RAY DIFFRACTIONr_chiral_restr0.0890.21251
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215657
X-RAY DIFFRACTIONr_mcbond_it0.6851.55152
X-RAY DIFFRACTIONr_mcangle_it1.29628232
X-RAY DIFFRACTIONr_scbond_it2.35832437
X-RAY DIFFRACTIONr_scangle_it4.0954.52080
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 433 -
Rwork0.193 7768 -
all-8201 -
obs--99.64 %
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)
10.40530.0422-0.09770.3114-0.01110.2644-0.0067-0.0273-0.01410.01370.0032-0.05250.0070.03950.00350.0048-0.0114-0.00280.0376-0.00690.031187.3936-40.9006-1.4149
20.26630.02160.02230.3930.04250.2263-0.00410.01290.0525-0.02130.01390.0322-0.0361-0.0176-0.00980.0345-0.00840.00550.00620.0060.031764.3612-19.721.2106
30.4240.0956-0.1420.31310.04190.3301-0.07620.0267-0.066-0.05050.0418-0.03030.0844-0.06560.03450.0597-0.03560.00560.019-0.00750.015466.55-59.4333-9.0986
40.22370.1078-0.08050.363-0.08160.35450.0196-0.01540.01780.0164-0.00760.06970.0428-0.0659-0.0120.0119-0.0241-0.0020.04140.01210.021847.8549-41.79849.3132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 271
2X-RAY DIFFRACTION2B12 - 271
3X-RAY DIFFRACTION3C13 - 271
4X-RAY DIFFRACTION4D12 - 271

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