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- PDB-7rml: Neisseria meningitidis Methylenetetrahydrofolate reductase in com... -

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Basic information

Entry
Database: PDB / ID: 7rml
TitleNeisseria meningitidis Methylenetetrahydrofolate reductase in complex with FAD
Components5,10-methylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methylenetetrahydrofolate reductase [NAD(P)H] activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / 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
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsPederick, J.L. / Wegener, K.L. / Salaemae, W. / Bruning, J.B.
CitationJournal: Protein Sci. / Year: 2023
Title: Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase.
Authors: Pantong, W. / Pederick, J.L. / Maenpuen, S. / Tinikul, R. / Jayapalan, J.J. / Jovcevski, B. / Wegener, K.L. / Bruning, J.B. / Salaemae, W.
History
DepositionJul 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)104,1436
Polymers101,7863
Non-polymers2,3573
Water543
1
B: 5,10-methylenetetrahydrofolate reductase
C: 5,10-methylenetetrahydrofolate reductase
hetero molecules

B: 5,10-methylenetetrahydrofolate reductase
C: 5,10-methylenetetrahydrofolate reductase
hetero molecules

A: 5,10-methylenetetrahydrofolate reductase
hetero molecules

A: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,28512
Polymers203,5726
Non-polymers4,7136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
Buried area24810 Å2
ΔGint-138 kcal/mol
Surface area61900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.444, 146.598, 86.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 through 6 and (name N...
21(chain B and ((resid 3 through 6 and (name N...
31(chain C and ((resid 3 through 6 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRGLUGLU(chain A and ((resid 3 through 6 and (name N...AA3 - 63 - 6
12ASNASNFADFAD(chain A and ((resid 3 through 6 and (name N...AA - D2 - 3012
13ASNASNFADFAD(chain A and ((resid 3 through 6 and (name N...AA - D2 - 3012
14ASNASNFADFAD(chain A and ((resid 3 through 6 and (name N...AA - D2 - 3012
15ASNASNFADFAD(chain A and ((resid 3 through 6 and (name N...AA - D2 - 3012
21TYRTYRGLUGLU(chain B and ((resid 3 through 6 and (name N...BB3 - 63 - 6
22TYRTYRPROPRO(chain B and ((resid 3 through 6 and (name N...BB3 - 2923 - 292
23TYRTYRPROPRO(chain B and ((resid 3 through 6 and (name N...BB3 - 2923 - 292
24TYRTYRPROPRO(chain B and ((resid 3 through 6 and (name N...BB3 - 2923 - 292
25TYRTYRPROPRO(chain B and ((resid 3 through 6 and (name N...BB3 - 2923 - 292
31TYRTYRGLUGLU(chain C and ((resid 3 through 6 and (name N...CC3 - 63 - 6
32TYRTYRPROPRO(chain C and ((resid 3 through 6 and (name N...CC3 - 2923 - 292
33TYRTYRPROPRO(chain C and ((resid 3 through 6 and (name N...CC3 - 2923 - 292
34TYRTYRPROPRO(chain C and ((resid 3 through 6 and (name N...CC3 - 2923 - 292
35TYRTYRPROPRO(chain C and ((resid 3 through 6 and (name N...CC3 - 2923 - 292

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Components

#1: Protein 5,10-methylenetetrahydrofolate reductase


Mass: 33928.637 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: metF, NMB0943 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9JZQ3, methylenetetrahydrofolate reductase [NAD(P)H]
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 10 - 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→44.6 Å / Num. obs: 25042 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Net I/σ(I): 20.9 / Num. measured all: 339610 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.8313.40.9414433633120.9110.2660.9783100
8.96-44.612.10.02992177610.9990.0080.0370.299.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UME

5ume


Resolution: 2.7→43.45 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1255 5.02 %
Rwork0.2344 23742 -
obs0.2366 24997 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.24 Å2 / Biso mean: 82.0208 Å2 / Biso min: 55.18 Å2
Refinement stepCycle: final / Resolution: 2.7→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 0 159 3 6163
Biso mean--88.62 64.66 -
Num. residues----809
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1947X-RAY DIFFRACTION11.523TORSIONAL
12B1947X-RAY DIFFRACTION11.523TORSIONAL
13C1947X-RAY DIFFRACTION11.523TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.810.39051350.318726122747
2.81-2.940.37571250.311626022727
2.94-3.090.35741380.299426072745
3.09-3.280.33981460.297926042750
3.28-3.540.30981180.269926272745
3.54-3.890.28931530.234426102763
3.89-4.460.28251410.211126632804
4.46-5.610.24481460.20826542800
5.61-43.450.24021530.211827632916
Refinement TLS params.Method: refined / Origin x: -38.4358 Å / Origin y: -32.0464 Å / Origin z: -3.1064 Å
111213212223313233
T0.708 Å2-0.0382 Å20.0694 Å2-0.7638 Å2-0.0745 Å2--0.6999 Å2
L0.2942 °20.5243 °20.4896 °2-0.5049 °20.0851 °2--0.1103 °2
S0.1062 Å °0.0358 Å °0.0948 Å °0.1941 Å °-0.1682 Å °0.0648 Å °0.1116 Å °0.0058 Å °0.0641 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 301
2X-RAY DIFFRACTION1allB3 - 292
3X-RAY DIFFRACTION1allB301
4X-RAY DIFFRACTION1allC3 - 292
5X-RAY DIFFRACTION1allC301
6X-RAY DIFFRACTION1allD1 - 3

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