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- PDB-1gq2: Malic Enzyme from Pigeon Liver -

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Basic information

Entry
Database: PDB / ID: 1gq2
TitleMalic Enzyme from Pigeon Liver
ComponentsMALIC ENZYME
KeywordsOXIDOREDUCTASE / MALIC ENZYME / PIGEON LIVER / NADP-DEPENDENT / NAD-NADP SELECTIVITY / DECARBOXYLASE / MALATE / MN2+
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / NAD binding / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, N-terminal 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, N-terminal 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXALATE ION / NADP-dependent malic enzyme
Similarity search - Component
Biological speciesCOLUMBA LIVIA (rock pigeon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, Z. / Zhang, H. / Liang, T.
CitationJournal: Protein Sci. / Year: 2002
Title: Structural Studies of the Pigeon Cytosolic Nadp+ -Dependent Malic Enzyme
Authors: Yang, Z. / Zhang, H. / Huang, H.-C. / Kuo, C.-C. / Tsai, L.-C. / Yuan, H.S. / Chou, W.-Y. / Chang, G.-G. / Tong, L.
History
DepositionNov 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id

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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
E: MALIC ENZYME
F: MALIC ENZYME
G: MALIC ENZYME
H: MALIC ENZYME
I: MALIC ENZYME
J: MALIC ENZYME
K: MALIC ENZYME
L: MALIC ENZYME
M: MALIC ENZYME
N: MALIC ENZYME
O: MALIC ENZYME
P: MALIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,016,764133
Polymers1,000,58416
Non-polymers16,179117
Water18,8981049
1
A: MALIC ENZYME
B: MALIC ENZYME
C: MALIC ENZYME
D: MALIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,00727
Polymers250,1464
Non-polymers3,86123
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: MALIC ENZYME
F: MALIC ENZYME
G: MALIC ENZYME
H: MALIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,12431
Polymers250,1464
Non-polymers3,97827
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
I: MALIC ENZYME
J: MALIC ENZYME
K: MALIC ENZYME
L: MALIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,14931
Polymers250,1464
Non-polymers4,00227
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
M: MALIC ENZYME
N: MALIC ENZYME
O: MALIC ENZYME
P: MALIC ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,48544
Polymers250,1464
Non-polymers4,33940
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.149, 140.863, 167.079
Angle α, β, γ (deg.)90.05, 87.16, 75.63
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
MALIC ENZYME


Mass: 62536.523 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: NADP+, OXALATE, MN2+ / Source: (gene. exp.) COLUMBA LIVIA (rock pigeon) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P40927, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)

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Non-polymers , 6 types, 1166 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Cl
#6: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHERE ARE 3 CIS-PRO FROM CHAIN A TO CHAIN P. THE PROLINES IN CIS CONFORMATIONS ARE: PRO 114, PRO 422, PRO 544.
Has protein modificationY
Sequence detailsTHE SEQUENCES WAS RENUMBERED TO 23-580

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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: 2.94 Å3/Da / Density % sol: 57.9 %
Crystal growpH: 5.5 / Details: 100 MM SODIUM CITRATE, PH 5.5, 8% PEG6000, 1M LICL
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlpigeon ME1drop
220 mMTris1droppH7.4
310 mMoxalate1drop
45 mM1dropMnCl2
50.23 mMNADP+1drop
62 mMdithiothreitol1drop
7100 mMsodium citrate1reservoirpH5.5
88 %PEG60001reservoir
91 M1reservoirLiCl

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.176
DetectorType: ADSC Q-4 / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.176 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 334606 / % possible obs: 88.2 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.6 / % possible all: 76
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 314771 / % possible obs: 83 % / Num. measured all: 570674
Reflection shell
*PLUS
Lowest resolution: 2.6 Å / % possible obs: 76 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB

Resolution: 2.5→10 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 23235 7.5 %RANDOM
Rwork0.21 ---
obs0.21 309710 83 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.1018 Å2 / ksol: 0.419231 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-14.02 Å2-5.44 Å2-0.31 Å2
2---6.03 Å2-0.39 Å2
3----7.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms69521 0 949 1049 71519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 2.5→2.52 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.347 350 7.2 %
Rwork0.297 4517 -
obs--65.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.NADP1WATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMTOP.OXL
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.211 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Lowest resolution: 2.6 Å / Rfactor Rfree: 0.342 / Rfactor Rwork: 0.302 / Rfactor obs: 0.302

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