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- PDB-4dpl: Structure of malonyl-coenzyme A reductase from crenarchaeota in c... -

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Basic information

Entry
Database: PDB / ID: 4dpl
TitleStructure of malonyl-coenzyme A reductase from crenarchaeota in complex with NadP
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 ...: / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Unknown ligand / Malonyl-CoA reductase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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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)161,41312
Polymers158,4394
Non-polymers2,9748
Water15,979887
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17610 Å2
ΔGint-119 kcal/mol
Surface area46650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.580, 128.800, 140.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.984063, -0.10812, 0.141176), (-0.10746, -0.994133, -0.012317), (0.14168, -0.00305, -0.989908)3.44574, 3.6673, -45.35931
3given(-0.99784, 0.065457, 0.005559), (0.056835, 0.817778, 0.57272), (0.032942, 0.571799, -0.819732)127.93306, 6.67289, -34.60421
4given(-0.985888, 0.055542, -0.157925), (0.043573, -0.825706, -0.562415), (-0.161637, -0.561359, 0.811634)124.19424, -15.75407, 5.925

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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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 33% PEP 426, 0.1 M NaOAc, 0.15 M (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 135044 / Num. obs: 135044 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.579 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0095refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YS4

1ys4


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.692 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19411 6764 5 %RANDOM
Rwork0.16332 ---
obs0.1649 127753 99.5 %-
all-128183 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.979 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2--0.11 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10961 0 216 887 12064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02211459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.821.97915501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7151421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.21764
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028147
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 452 -
Rwork0.253 8728 -
obs--98.28 %
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)
10.9299-0.2581-0.15331.50270.69851.2503-0.08840.01310.0385-0.00670.03520.03650.083-0.07240.05330.0175-0.0142-0.00320.03730.00230.010347.282-0.55-19.458
21.12550.1661-0.05841.69710.22560.7087-0.0295-0.1351-0.08260.0040.0447-0.16440.05650.0912-0.01520.01170.0222-0.01180.0718-0.01060.051980.633-2.579-16.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 360
2X-RAY DIFFRACTION1B6 - 360
3X-RAY DIFFRACTION1A401
4X-RAY DIFFRACTION1B401
5X-RAY DIFFRACTION2C6 - 360
6X-RAY DIFFRACTION2D6 - 360
7X-RAY DIFFRACTION2C401
8X-RAY DIFFRACTION2D401

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