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- PDB-1zp3: E. coli Methylenetetrahydrofolate Reductase (oxidized) -

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Basic information

Entry
Database: PDB / ID: 1zp3
TitleE. coli Methylenetetrahydrofolate Reductase (oxidized)
Components5,10-methylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM BARREL / FLAVIN / REDUCTASE
Function / homology
Function and homology information


methylenetetrahydrofolate reductase [NAD(P)H] / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / protein-folding chaperone binding / protein-containing complex / cytosol
Similarity search - Function
5,10-methylenetetrahydrofolate reductase / Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / TIM Barrel - #220 / FAD-linked oxidoreductase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 5,10-methylenetetrahydrofolate reductase / 5,10-methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPejchal, R. / Sargeant, R. / Ludwig, M.L.
CitationJournal: Biochemistry / Year: 2005
Title: Structures of NADH and CH(3)-H(4)Folate Complexes of Escherichia coli Methylenetetrahydrofolate Reductase Reveal a Spartan Strategy for a Ping-Pong Reaction
Authors: Pejchal, R. / Sargeant, R. / Ludwig, M.L.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: 5,10-methylenetetrahydrofolate reductase
B: 5,10-methylenetetrahydrofolate reductase
C: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,74313
Polymers102,6483
Non-polymers3,09510
Water7,837435
1
A: 5,10-methylenetetrahydrofolate reductase
C: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5279
Polymers68,4322
Non-polymers2,0967
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: 5,10-methylenetetrahydrofolate reductase
C: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5279
Polymers68,4322
Non-polymers2,0967
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-93 kcal/mol
Surface area22870 Å2
MethodPISA
3
B: 5,10-methylenetetrahydrofolate reductase
hetero molecules

B: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4318
Polymers68,4322
Non-polymers2,0006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)103.236, 127.789, 97.703
Angle α, β, γ (deg.)90.00, 121.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-930-

HOH

21C-533-

HOH

31C-823-

HOH

DetailsThe biological assembly is a tetramer. It can be generated from the trimer in the asymmetric unit (A,B,C) by the operations: -y, x, -z. A unique tetramer (A,B,B',C' or A',B',B,C) can be picked from the resulting hexamer (A,B,C,A',B',C').

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Components

#1: Protein 5,10-methylenetetrahydrofolate reductase


Mass: 34215.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metF / Plasmid: pET23B / Production host: Escherichia coli (E. coli)
References: UniProt: P00394, UniProt: P0AEZ1*PLUS, EC: 1.7.99.5
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→19.91 Å / Num. all: 91751 / Num. obs: 91236 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.8 Å2 / Net I/σ(I): 21.6
Reflection shellResolution: 1.85→1.97 Å / Mean I/σ(I) obs: 4.2 / Num. unique all: 13534 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B5T

1b5t


Resolution: 1.85→19.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2180544.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 9117 10 %RANDOM
Rwork0.214 ---
all0.229 91751 --
obs0.214 91236 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9512 Å2 / ksol: 0.35167 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-3.15 Å2
2--1.73 Å20 Å2
3----1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 203 435 7110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 1467 9.8 %
Rwork0.276 13534 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param.fadtoph.fad
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5param.mpdtoph.mpd

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