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

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Basic information

Entry
Database: PDB / ID: 4dpm
TitleStructure of malonyl-coenzyme A reductase from crenarchaeota in complex with CoA
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
COENZYME A / Malonyl-CoA reductase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / pdbx_struct_conn_angle / struct_conn / 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_atom_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_atom_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_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
E: Malonyl-CoA/succinyl-CoA reductase
F: Malonyl-CoA/succinyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,40918
Polymers237,6586
Non-polymers4,75112
Water9,980554
1
A: Malonyl-CoA/succinyl-CoA reductase
B: Malonyl-CoA/succinyl-CoA reductase
hetero molecules

A: Malonyl-CoA/succinyl-CoA reductase
B: Malonyl-CoA/succinyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,60612
Polymers158,4394
Non-polymers3,1678
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area17360 Å2
ΔGint-119 kcal/mol
Surface area46710 Å2
MethodPISA
2
C: Malonyl-CoA/succinyl-CoA reductase
D: Malonyl-CoA/succinyl-CoA reductase
E: Malonyl-CoA/succinyl-CoA reductase
F: Malonyl-CoA/succinyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,60612
Polymers158,4394
Non-polymers3,1678
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17440 Å2
ΔGint-114 kcal/mol
Surface area47560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.630, 137.620, 362.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999986, 0.000881, -0.005205), (0.000935, -0.940797, -0.338969), (-0.005196, -0.338969, 0.940783)-37.34821, 0.02611, -0.21757
3given(0.400436, 0.902074, 0.160978), (0.902638, -0.41857, 0.100213), (0.157781, 0.105176, -0.981857)-0.38154, -19.33106, 113.02699
4given(-0.586196, -0.537641, -0.606067), (-0.527458, -0.314553, 0.789205), (-0.614949, 0.782303, -0.099193)65.30096, -34.04035, 73.92091

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Components

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


Mass: 39609.727 Da / Num. of mol.: 6
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 11% PEG 6000, 10 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 108682 / Num. obs: 108682 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069 / Net I/σ(I): 17.8
Reflection shellResolution: 2.3→2.36 Å / Rsym value: 0.49 / % possible all: 54.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0095refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YS4

1ys4


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.025 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 5498 5.1 %RANDOM
Rwork0.19817 ---
obs0.20066 103125 87.91 %-
all-103125 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16436 0 294 554 17284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02217133
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3371.97623165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52752122
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_restr0.1660.22633
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212173
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 242 -
Rwork0.39 4316 -
obs--51.24 %
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)
11.69150.3347-0.75191.1697-0.14934.1593-0.2093-0.12620.0786-0.32230.0486-0.1036-1.06290.78120.16061.188-0.1029-0.09620.7017-0.03270.319212.8212.29546.115
21.03350.328-0.29952.14871.38554.7480.0795-0.5466-0.32970.0011-0.104-0.5459-0.00561.58610.02450.5780.22990.01731.40010.25870.517123.269-8.28570.987
33.0756-0.47340.36821.7071-0.55481.9259-0.2018-0.3623-0.44930.31440.29660.19780.3233-0.052-0.09470.27160.14380.07780.11920.09760.3643-7.665-26.29516.142
42.7781-0.6346-0.54241.39750.05942.2641-0.2012-0.4890.20650.44860.2590.1234-0.18610.1074-0.05790.28990.17230.04130.17080.0040.3772-29.77619.24224.19
51.7184-0.1787-0.01131.6322-0.16621.2133-0.16430.0915-0.1705-0.04960.1668-0.22040.18210.2959-0.00250.07450.03860.02640.11-0.0320.22363.81-11.9330.676
61.0564-0.0506-0.16771.41630.49441.3868-0.15450.01920.12010.04410.12690.4449-0.2248-0.37130.02760.08170.08980.00860.15920.11710.4455-41.15310.9784.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C6 - 359
2X-RAY DIFFRACTION1D6 - 359
3X-RAY DIFFRACTION1C401 - 402
4X-RAY DIFFRACTION1D401 - 402
5X-RAY DIFFRACTION2E7 - 359
6X-RAY DIFFRACTION2F7 - 359
7X-RAY DIFFRACTION2E401 - 402
8X-RAY DIFFRACTION2F401 - 402
9X-RAY DIFFRACTION3A6 - 156
10X-RAY DIFFRACTION3A334 - 359
11X-RAY DIFFRACTION3A401 - 402
12X-RAY DIFFRACTION4B6 - 156
13X-RAY DIFFRACTION4B334 - 359
14X-RAY DIFFRACTION4B401 - 402
15X-RAY DIFFRACTION5A157 - 333
16X-RAY DIFFRACTION6B157 - 333

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