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- PDB-1b5t: ESCHERICHIA COLI METHYLENETETRAHYDROFOLATE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1b5t
TitleESCHERICHIA COLI METHYLENETETRAHYDROFOLATE REDUCTASE
ComponentsPROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)
KeywordsOXIDOREDUCTASE / BETA ALPHA BARREL / 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 / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGuenther, B.D. / Sheppard, C.A. / Tran, P. / Rozen, R. / Matthews, R.G. / Ludwig, M.L.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The structure and properties of methylenetetrahydrofolate reductase from Escherichia coli suggest how folate ameliorates human hyperhomocysteinemia.
Authors: Guenther, B.D. / Sheppard, C.A. / Tran, P. / Rozen, R. / Matthews, R.G. / Ludwig, M.L.
History
DepositionJan 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_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 / _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: PROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)
B: PROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)
C: PROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3059
Polymers92,3463
Non-polymers2,9586
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.000, 128.200, 98.200
Angle α, β, γ (deg.)90.00, 121.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)


Mass: 30782.102 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: METF / Production host: Escherichia coli (E. coli)
References: UniProt: P00394, UniProt: P0AEZ1*PLUS, EC: 1.7.99.5
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.1 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %isopropanol11
2100 mMMES11
30.040 mMFAD11
4160 mMammonium sulfate11
58-13 %PEG800011

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.012, 1.010, 1.008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0121
21.011
31.0081
ReflectionResolution: 2.5→30 Å / Num. obs: 36508 / % possible obs: 97.3 % / Biso Wilson estimate: 26.3 Å2 / Rsym value: 0.068 / Net I/σ(I): 22
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 10 / Rsym value: 0.101 / % possible all: 83
Reflection
*PLUS
Num. measured all: 377615 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 83 % / Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3604 9.9 %RANDOM
Rwork0.212 ---
obs0.212 36351 97 %-
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 162 184 6564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.611.5
X-RAY DIFFRACTIONx_mcangle_it2.722
X-RAY DIFFRACTIONx_scbond_it2.592
X-RAY DIFFRACTIONx_scangle_it3.92.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 500 9.2 %
Rwork0.292 4940 -
obs--86.9 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.292

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