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- PDB-4dpk: Structure of malonyl-coenzyme A reductase from crenarchaeota -

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Basic information

Entry
Database: PDB / ID: 4dpk
TitleStructure of malonyl-coenzyme A reductase from crenarchaeota
ComponentsMalonyl-CoA/succinyl-CoA reductase
KeywordsOXIDOREDUCTASE / dinucleotide binding / dimerization domain / reductase / NadP / CoA
Function / homology
Function and homology information


malonyl-CoA reductase (malonate semialdehyde-forming) / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / NAD binding / NADP binding / protein dimerization activity / RNA binding
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Malonyl-CoA reductase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDemmer, U. / Warkentin, E. / Srivastava, A. / Kockelkorn, D. / Fuchs, G. / Ermler, U.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for a Bispecific NADP+ and CoA Binding Site in an Archaeal Malonyl-Coenzyme A Reductase.
Authors: Demmer, U. / Warkentin, E. / Srivastava, A. / Kockelkorn, D. / Potter, M. / Marx, A. / Fuchs, G. / Ermler, U.
History
DepositionFeb 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Mar 20, 2013Group: Database references
Revision 1.4Sep 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Malonyl-CoA/succinyl-CoA reductase
B: Malonyl-CoA/succinyl-CoA reductase
C: Malonyl-CoA/succinyl-CoA reductase
D: Malonyl-CoA/succinyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,57916
Polymers158,4394
Non-polymers1,14012
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-151 kcal/mol
Surface area48020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.090, 81.940, 124.610
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEUDD8 - 1338 - 133
21LEULEULEULEUAA8 - 1338 - 133
31LEULEULEULEUBB8 - 1338 - 133
41LEULEULEULEUCC8 - 1338 - 133
12GLNGLNGLYGLYDD137 - 355137 - 355
22GLNGLNGLYGLYAA137 - 355137 - 355
32GLNGLNGLYGLYBB137 - 355137 - 355
42GLNGLNGLYGLYCC137 - 355137 - 355

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Components

#1: Protein
Malonyl-CoA/succinyl-CoA reductase


Mass: 39609.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: mcr/scr, STK_21710 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96YK1, malonyl-CoA reductase (malonate semialdehyde-forming), succinate-semialdehyde dehydrogenase (acylating)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 34% MPD,0.1 M HEPES,100 mM CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 107988 / Num. obs: 107988 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.059 / Net I/σ(I): 13.8
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.377 / % possible all: 56.8

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Processing

Software
NameVersionClassification
EPMRphasing
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YS4

1ys4


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.823 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23069 4865 5 %RANDOM
Rwork0.18463 ---
obs0.18695 93051 95.86 %-
all-98649 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.024 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å21.23 Å2
2---1.66 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10972 0 60 500 11532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02211302
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.96115258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70951416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13524.148458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1461570
X-RAY DIFFRACTIONr_chiral_restr0.1080.21734
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028050
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.25325
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.27693
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2690
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7191.57285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.106211526
X-RAY DIFFRACTIONr_scbond_it1.95234489
X-RAY DIFFRACTIONr_scangle_it2.9724.53832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2657 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Dloose positional0.285
2Aloose positional0.285
3Bloose positional0.255
4Cloose positional0.265
1Dloose thermal1.8310
2Aloose thermal1.3110
3Bloose thermal2.0810
4Cloose thermal1.9410
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 267 -
Rwork0.231 5276 -
obs--74.37 %
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)
11.50440.2384-0.2971.75880.03331.5959-0.0389-0.0249-0.00110.1965-0.00290.1157-0.0162-0.19760.04180.0571-0.0275-0.01720.08560.00740.052118.702-0.41741.025
20.6446-0.309-0.24482.7268-0.10250.89270.05070.1413-0.0265-0.4793-0.10890.07480.0916-0.11970.05810.1672-0.0455-0.03640.1151-0.02630.054824.293-14.05110.844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 359
2X-RAY DIFFRACTION1B6 - 359
3X-RAY DIFFRACTION2C6 - 359
4X-RAY DIFFRACTION2D6 - 359

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