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- PDB-4gi2: Crotonyl-CoA Carboxylase/Reductase -

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Basic information

Entry
Database: PDB / ID: 4gi2
TitleCrotonyl-CoA Carboxylase/Reductase
ComponentsCrotonyl-CoA carboxylase/reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / reductive Carboxylation / NADPH / Dehydrogenase/Reductase
Function / homology
Function and homology information


crotonyl-CoA reductase activity / nucleotide 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 / GroES-like superfamily ...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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Crotonyl-CoA carboxylase/reductase
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWeidenweber, S. / Erb, T.J. / Ermler, U.
CitationJournal: To be Published
Title: Crotonyl-CoA Carboxylase/Reductase
Authors: Weidenweber, S. / Erb, T.J. / Ermler, U.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: Crotonyl-CoA carboxylase/reductase
B: Crotonyl-CoA carboxylase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2525
Polymers97,7412
Non-polymers1,5113
Water0
1
A: Crotonyl-CoA carboxylase/reductase
hetero molecules

A: Crotonyl-CoA carboxylase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2766
Polymers97,7412
Non-polymers1,5354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6150 Å2
ΔGint-46 kcal/mol
Surface area31360 Å2
MethodPISA
2
B: Crotonyl-CoA carboxylase/reductase
hetero molecules

B: Crotonyl-CoA carboxylase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2274
Polymers97,7412
Non-polymers1,4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5770 Å2
ΔGint-26 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.400, 91.400, 206.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 9:433 ) AND (NOT ELEMENT H)
21CHAIN B AND (RESSEQ 9:433 ) AND (NOT ELEMENT H)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 9:433 ) AND (NOT ELEMENT H)A0
211CHAIN B AND (RESSEQ 9:433 ) AND (NOT ELEMENT H)B0

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Components

#1: Protein Crotonyl-CoA carboxylase/reductase / / CCR


Mass: 48870.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: ccr / Plasmid: pET23-b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: C5AP81
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4M Sodium formate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 76 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 20867 / % possible obs: 97.2 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Biso Wilson estimate: 81.05 Å2
Reflection shellResolution: 3→3.1 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
SHELXDphasing
SHARPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KRT, 3HZZ

3krt

3hzz


Resolution: 3→43.182 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7977 / SU ML: 0.44 / σ(F): 1.36 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1039 5.04 %Random
Rwork0.182 ---
all0.185 ---
obs0.185 20597 99.61 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.861 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 267.9 Å2 / Biso mean: 88.4874 Å2 / Biso min: 36.72 Å2
Baniso -1Baniso -2Baniso -3
1-7.6206 Å20 Å2-0 Å2
2--7.6206 Å20 Å2
3----15.2412 Å2
Refinement stepCycle: LAST / Resolution: 3→43.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 97 0 6729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096923
X-RAY DIFFRACTIONf_angle_d1.2529426
X-RAY DIFFRACTIONf_chiral_restr0.077984
X-RAY DIFFRACTIONf_plane_restr0.0041216
X-RAY DIFFRACTIONf_dihedral_angle_d18.5992479
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3305X-RAY DIFFRACTIONPOSITIONAL0.055
12B3305X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0002-3.15840.38211370.29627652902100
3.1584-3.35620.3491410.250827392880100
3.3562-3.61520.28081580.212727632921100
3.6152-3.97880.26891580.177427612919100
3.9788-4.5540.19191420.140927642906100
4.554-5.73540.22581610.17012803296499
5.7354-43.18670.2051420.17112963310599
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)
11.2310.3960.32442.331-0.7343.5224-0.30910.07590.1923-0.0603-0.20350.05050.0125-0.9710.38690.4533-0.0058-0.18651.0119-0.14220.5366-2.68150.6923-33.6383
23.11791.15772.41371.21640.10895.1788-0.31630.3484-0.0957-0.18140.1393-0.2-0.206-0.32970.15470.40930.15220.0020.6859-0.1130.50556.950250.0295-22.0255
30.3799-0.52090.19940.788-0.0940.61240.57920.752-0.2331-0.3363-0.3835-0.5540.98161.0811-0.46490.66550.37960.15030.7751-0.16830.592626.501234.9884-18.3284
40.9999-0.691-0.27271.0320.86812.15650.56240.6333-0.44950.2728-0.67450.37350.89850.33680.01931.41960.2784-0.37151.0407-0.35890.847323.826118.8547-11.8994
51.5517-0.49380.95590.214-0.43710.83770.34940.3841-0.95140.073-0.05150.03321.09160.59260.58180.73580.6653-0.03350.1496-0.25740.384225.240823.945-7.1304
61.10370.1631.17010.31710.47023.9208-0.00250.4992-0.0855-0.2898-0.13670.09250.42180.78670.14640.22850.09680.01950.9107-0.01830.606322.036739.7893-15.4081
73.94771.03750.24096.25240.17954.2217-0.10471.0279-0.4776-0.1877-0.0265-0.45550.78510.02180.13940.37060.18190.03970.7514-0.26160.44037.67240.2753-37.3694
83.2159-2.69913.27335.5916-2.4256.28790.07730.0032-0.2439-0.7587-0.05920.8308-0.2168-0.86950.15250.65770.40270.02130.6031-0.15390.786-13.444678.86433.8071
90.1736-0.66540.16892.7312-0.80040.93020.45430.35360.2185-0.4872-0.2466-0.2729-0.8728-0.3355-0.04591.01190.3660.1380.44640.03350.68456.513783.7074-3.1228
102.4643-1.1575-0.42212.03190.90411.28060.13260.18010.0424-0.1322-0.15370.639-0.2163-0.2967-0.03910.21970.3996-0.13610.4214-0.17020.50278.192470.2951-5.2118
113.2713-1.6436-0.45072.60590.77171.7119-0.3106-0.5650.16660.28280.3681-0.2894-0.55360.1126-0.0860.4530.0699-0.0470.312-0.04450.375318.896567.535812.483
122.1493-0.4012-0.61241.569-0.1812.99-0.2519-0.78870.27330.05030.60730.2191-0.47720.2569-0.24470.71540.2009-0.06710.4881-0.26910.725540.139675.896916.1668
132.987-0.34451.57961.44620.35733.183-0.8253-0.60990.54710.46710.6172-0.9045-0.62190.64860.27620.39030.0845-0.14710.7307-0.27340.760940.356870.045812.1338
142.4044-0.0132-0.15521.0249-0.47711.766-0.0077-0.10510.54580.28450.12240.2542-0.3969-0.07540.35380.15650.306-0.0413-0.09610.08290.377223.095865.69478.4765
152.96820.4370.60322.53580.58132.11710.2334-0.1656-0.0470.4581-0.0057-0.1862-0.4501-0.5578-0.12740.81710.24110.00390.3359-0.01830.43994.180983.511111.9662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 8:65)A8 - 65
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 66:189)A66 - 189
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 190:253)A190 - 253
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 254:276)A254 - 276
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 277:342)A277 - 342
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 343:385)A343 - 385
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 386:434)A386 - 434
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 9:27)B9 - 27
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 28:93)B28 - 93
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 94:165)B94 - 165
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 166:253)B166 - 253
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 254:276)B254 - 276
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 277:342)B277 - 342
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 343:385)B343 - 385
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 386:434)B386 - 434

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