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- PDB-6c7n: Monoclinic form of malic enzyme from sorghum at 2 angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 6c7n
TitleMonoclinic form of malic enzyme from sorghum at 2 angstroms resolution
ComponentsMalic enzyme
KeywordsOXIDOREDUCTASE / enzyme substrate complex
Function / homology
Function and homology information


malate dehydrogenase (decarboxylating) (NADP+) activity / malate metabolic process / pyruvate metabolic process / chloroplast / NAD binding / metal ion binding
Similarity search - Function
Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain ...Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / PYRUVIC ACID / Malic enzyme
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTrajtenberg, F. / Alvarez, C. / Buschiazzo, A.
CitationJournal: Nat.Plants / Year: 2019
Title: Molecular adaptations of NADP-malic enzyme for its function in C4photosynthesis in grasses.
Authors: Alvarez, C.E. / Bovdilova, A. / Hoppner, A. / Wolff, C.C. / Saigo, M. / Trajtenberg, F. / Zhang, T. / Buschiazzo, A. / Nagel-Steger, L. / Drincovich, M.F. / Lercher, M.J. / Maurino, V.G.
History
DepositionJan 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malic enzyme
B: Malic enzyme
C: Malic enzyme
D: Malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,02029
Polymers269,1104
Non-polymers4,91025
Water30,8961715
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26240 Å2
ΔGint-71 kcal/mol
Surface area67400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.100, 64.260, 202.720
Angle α, β, γ (deg.)90.000, 93.650, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Malic enzyme


Mass: 67277.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_3003G036200 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84LQ5

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Non-polymers , 5 types, 1740 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1715 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M KF, 30% (w/v) PEG3350, 2mM NADP, 2mM DTT, 40mM pyruvate 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 12, 2013 / Details: Varimax-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→35.24 Å / Num. obs: 181154 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.052 / Rrim(I) all: 0.1 / Net I/σ(I): 9.1 / Num. measured all: 665459 / Scaling rejects: 10
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.585 / Num. measured all: 31790 / Num. unique obs: 8879 / CC1/2: 0.733 / Rpim(I) all: 0.36 / Rrim(I) all: 0.69 / Net I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1819 1 %RANDOM
Rwork0.18 ---
obs0.18 181074 100 %-
Displacement parametersBiso max: 112.87 Å2 / Biso mean: 33.42 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.9008 Å20 Å2-0.7676 Å2
2---4.8507 Å20 Å2
3---3.9499 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 2→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15643 0 377 1727 17747
Biso mean--41.15 41.04 -
Num. residues----2030
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5971SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3038HARMONIC5
X-RAY DIFFRACTIONt_it17485HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2273SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22188SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17485HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg23802HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion16.2
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2516 121 0.91 %
Rwork0.211 13176 -
all0.2114 13297 -
obs--99.93 %
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)
10.61910.2234-0.16020.5390.24930.68060.001-0.0582-0.04160.05740.0084-0.04610.03860.0167-0.00950.00560.0034-0.0245-0.07410.00250.0293-43.2508-15.448937.3794
20.6262-0.0881-0.08350.67310.14660.4236-0.0158-0.03710.0144-0.01310.0060.0205-0.09050.0620.0099-0.0017-0.0181-0.0163-0.07070.00250.0116-39.03096.463934.8827
31.39330.0104-0.32550.31780.44021.04740.0144-0.14860.16570.01430.0326-0.0228-0.1470.1991-0.047-0.0168-0.0566-0.0217-0.034-0.0133-0.0154-25.678611.98141.9663
41.9258-0.09460.45980.91520.0511.5581-0.09090.28240.2449-0.10060.1231-0.125-0.28810.3864-0.0322-0.1146-0.13980.01510.0875-0.011-0.0595-6.551816.922926.9881
51.51150.2798-0.15450.6117-0.0582.8164-0.05280.4149-0.2179-0.1370.1185-0.13260.16270.5145-0.0657-0.1393-0.0217-0.00280.0686-0.091-0.0593-12.7410.836923.1634
61.92750.5994-0.70961.4664-0.62881.3271-0.05310.0659-0.3825-0.09330.0405-0.27070.0730.3320.0126-0.13430.0237-0.02380.0121-0.01140.0205-13.0144-4.438638.8181
71.26291.5955-0.37490.96020.64261.0019-0.0108-0.2286-0.1710.0522-0.0329-0.06830.00770.11440.0437-0.00240.0258-0.0901-0.0470.0790.0359-26.7319-11.920350.895
80.48780.2873-0.12620.56450.1270.9481-0.0162-0.04750.01860.024-0.0072-0.0078-0.0255-0.0280.0235-0.0024-0.0012-0.0143-0.07260.00670.0299-56.3315-3.455832.9435
90.45290.19190.25370.5246-0.11190.6582-0.0189-0.0515-0.03820.048-0.0134-0.05590.0863-0.06950.0323-0.0032-0.01430.0015-0.0869-0.00180.0024-60.4092-27.024929.1216
100.5732-0.10460.10860.43430.16241.13880.0010.09210.0428-0.0414-0.0890.01510.009-0.16530.0879-0.0334-0.0028-0.0151-0.0423-0.0134-0.0112-74.656-26.81797.4306
110.22130.47640.41610.20620.27580.8438-0.0312-0.05620.02230.0091-0.0520.1332-0.0492-0.22340.0831-0.05140.02330.0022-0.0401-0.04720.0764-78.0209-7.536632.4737
120.6425-0.1754-0.06330.49450.08970.90180.0252-0.15860.00040.0631-0.06220.0035-0.0156-0.10460.037-0.0176-0.022-0.0228-0.0015-0.0194-0.0444-58.0244-1.065669.658
130.78820.07020.2280.49130.16351.40960.0504-0.1716-0.15890.1186-0.0851-0.07840.27710.11020.0347-0.0095-0.0018-0.0311-0.02360.0898-0.0931-45.0267-20.208876.2759
140.179-0.08930.25130.413-0.05481.3770.0086-0.2287-0.06230.23370.018-0.00090.06970.2706-0.0266-0.0325-0.0081-0.04890.12030.1094-0.168-32.876-9.874996.9618
150.02240.4507-0.24011.3739-0.99382.0151-0.0004-0.11140.0647-0.0084-0.0196-0.02330.1809-0.06990.02-0.0099-0.0275-0.0039-0.03820.0121-0.0271-61.1653-15.480156.6842
161.1625-0.37950.02641.2327-0.28231.1014-0.0161-0.2676-0.08350.1146-0.01220.10040.1385-0.13120.0283-0.0061-0.0721-0.00320.03310.0256-0.0822-67.8419-18.432473.1074
171.0085-0.09040.1510.7786-0.28081.3418-0.0235-0.24970.06370.0639-0.06590.0786-0.0654-0.23620.0894-0.0704-0.00760.00380.0524-0.0894-0.0735-78.0858-0.856966.081
180.3268-0.2435-0.38090.50110.42532.1117-0.0114-0.10180.23060.0327-0.03290.0974-0.2993-0.28660.0443-0.03510.0444-0.03010.008-0.091-0.0029-79.931910.093460.2441
191.55330.4595-0.45482.41881.34291.5726-0.0424-0.22260.26010.2033-0.15010.36250.0595-0.4890.1924-0.17530.02350.01730.1581-0.1566-0.0584-93.8336-1.213860.7962
202.2056-0.35230.31763.82382.35073.2649-0.029-0.4056-0.11330.6651-0.32080.50150.363-0.78510.3498-0.1547-0.11980.09150.1248-0.1138-0.105-96.697-13.982661.6729
210.4292-1.241-0.38870-0.43940.2548-0.0104-0.0796-0.0434-0.0116-0.05530.16350.1444-0.27220.0657-0.0417-0.0994-0.0397-0.012-0.0549-0.0083-83.0433-22.539653.3799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|84 - A|174 }A84 - 174
2X-RAY DIFFRACTION2{ A|175 - A|300 }A175 - 300
3X-RAY DIFFRACTION3{ A|301 - A|370 }A301 - 370
4X-RAY DIFFRACTION4{ A|371 - A|471 }A371 - 471
5X-RAY DIFFRACTION5{ A|472 - A|557 }A472 - 557
6X-RAY DIFFRACTION6{ A|558 - A|607 }A558 - 607
7X-RAY DIFFRACTION7{ A|608 - A|636 }A608 - 636
8X-RAY DIFFRACTION8{ B|84 - B|174 }B84 - 174
9X-RAY DIFFRACTION9{ B|175 - B|330 }B175 - 330
10X-RAY DIFFRACTION10{ B|331 - B|606 }B331 - 606
11X-RAY DIFFRACTION11{ B|607 - B|636 }B607 - 636
12X-RAY DIFFRACTION12{ C|84 - C|174 }C84 - 174
13X-RAY DIFFRACTION13{ C|175 - C|330 }C175 - 330
14X-RAY DIFFRACTION14{ C|331 - C|636 }C331 - 636
15X-RAY DIFFRACTION15{ D|83 - D|119 }D83 - 119
16X-RAY DIFFRACTION16{ D|120 - D|174 }D120 - 174
17X-RAY DIFFRACTION17{ D|175 - D|286 }D175 - 286
18X-RAY DIFFRACTION18{ D|287 - D|318 }D287 - 318
19X-RAY DIFFRACTION19{ D|319 - D|385 }D319 - 385
20X-RAY DIFFRACTION20{ D|386 - D|607 }D386 - 607
21X-RAY DIFFRACTION21{ D|608 - D|636 }D608 - 636

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