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- PDB-3hzz: 2.4 Angstrom Crystal Structure of Streptomyces collinus crotonyl ... -

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Basic information

Entry
Database: PDB / ID: 3hzz
Title2.4 Angstrom Crystal Structure of Streptomyces collinus crotonyl CoA carboxylase/reductase
ComponentsCrotonyl CoA reductase
KeywordsOXIDOREDUCTASE / Reductase / Carboxylase / alcohol dehydrogenase / biocatalysis / enoyl reductase / glyoxolate cycle / acetyl CoA assimilation / methylotrophy / serine cycle / polyketide
Function / homology
Function and homology information


crotonyl-CoA reductase / crotonyl-CoA reductase activity / NADP binding / metal ion binding
Similarity search - Function
Crotonyl-CoA reductase / : / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Crotonyl-CoA reductase / : / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Crotonyl-CoA reductase
Similarity search - Component
Biological speciesStreptomyces collinus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsScarsdale, J.N. / Musayev, F.N. / Wright, H.T.
Citation
Journal: To be Published
Title: Structure of Streptomycs collinus crotonyl COA carboxylase/reductase
Authors: Scarsdale, J.N. / Musayev, F.N. / Hazzard, C. / Florova, G. / Reynolds, K. / Wright, H.T.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase
Authors: Erb, T.J. / Brecht, V. / Fuchs, G. / Muller, M. / Alber, B.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: The ethylmalonyl-CoA pathway
Authors: Erb, T.J. / Berg, I.A. / Brecht, V. / Muller, M. / Fuchs, G. / Alber, B.E.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Crotonyl CoA reductase
B: Crotonyl CoA reductase
C: Crotonyl CoA reductase
D: Crotonyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,8729
Polymers206,3924
Non-polymers4805
Water10,539585
1
C: Crotonyl CoA reductase
D: Crotonyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3884
Polymers103,1962
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-45 kcal/mol
Surface area34900 Å2
MethodPISA
2
A: Crotonyl CoA reductase
B: Crotonyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4845
Polymers103,1962
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-55 kcal/mol
Surface area34760 Å2
MethodPISA
3
A: Crotonyl CoA reductase
D: Crotonyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3884
Polymers103,1962
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-42 kcal/mol
Surface area35420 Å2
MethodPISA
4
B: Crotonyl CoA reductase
C: Crotonyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4845
Polymers103,1962
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-51 kcal/mol
Surface area35820 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15550 Å2
ΔGint-99 kcal/mol
Surface area61470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.668, 134.380, 195.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthor-defined biological assembly is based on the fact that the dimer interface for dimers (A+B) as well as (C+D) is in a beta sheet. Size-exclusion chromatography indicates protein runs as a dimer

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Components

#1: Protein
Crotonyl CoA reductase


Mass: 51597.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces collinus (bacteria) / Gene: ccr, crotonyl COA reductase / Plasmid: pET28a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53865
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion with microseeding / pH: 6.2
Details: 0.1M MES, 2.0M Ammonium Sulfate, 3% PEG 200, pH 6.2, vapor diffusion with microseeding, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 13, 2008 / Details: Rigaku Varimax confocal optics
RadiationMonochromator: Rigaku Varimax Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→17.97 Å / Num. all: 82617 / Num. obs: 78199 / % possible obs: 94.7 % / Redundancy: 11.26 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 11.08 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 7.4 / Num. unique all: 8154 / Rsym value: 0.344 / % possible all: 92.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5.5.0088refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→17.97 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 21.702 / SU ML: 0.219
Isotropic thermal model: TLS with individual residual isotropic B factors
Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25712 2000 2.6 %RANDOM
Rwork0.20602 ---
obs0.20733 76039 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.779 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--0.27 Å2-0 Å2
3---1.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→17.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13692 0 25 585 14302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02114075
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.94619133
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47351791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35623.758636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.904152226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1091595
X-RAY DIFFRACTIONr_chiral_restr0.0710.22086
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110872
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3728886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.782514208
X-RAY DIFFRACTIONr_scbond_it1.4665189
X-RAY DIFFRACTIONr_scangle_it2.23694925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 141 -
Rwork0.317 5367 -
obs--92.91 %
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)
10.7425-0.0836-0.18860.68810.20951.45450.04910.186-0.1858-0.18490.0257-0.03630.07870.0338-0.07490.07810.0036-0.01630.0681-0.05890.066628.028344.1402109.6303
20.82140.0252-0.20240.5582-0.15841.38990.0609-0.0841-0.1170.0367-0.05040.09240.025-0.104-0.01060.0101-0.0148-0.0050.03750.00220.03682.25954.5541144.6014
30.8240.0070.37750.54180.07361.35170.0521-0.05990.01480.0246-0.0004-0.0962-0.06020.075-0.05160.0131-0.01490.00260.0186-0.0090.022141.998569.0084142.3592
41.2175-0.09020.27461.14440.34871.53120.06440.29580.2816-0.394-0.06670.0435-0.3318-0.10220.00230.17250.05560.00750.10220.05310.11911.234382.6893112.8364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 447
2X-RAY DIFFRACTION2B10 - 447
3X-RAY DIFFRACTION3C10 - 447
4X-RAY DIFFRACTION4D10 - 447

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