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- PDB-4zty: Neurospora crassa cobalamin-independent methionine synthase compl... -

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Basic information

Entry
Database: PDB / ID: 4zty
TitleNeurospora crassa cobalamin-independent methionine synthase complexed with Cd2+
ComponentsCobalamin-Independent Methionine synthase
KeywordsTRANSFERASE / homocysteine / methyltetrahydrofolate / tim barrel (alpha/beta barrel) / methionine synthesis / methyltransferase
Function / homology
Function and homology information


5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine biosynthetic process / methylation / zinc ion binding
Similarity search - Function
Cobalamin-independent methionine synthase / Cobalamin-independent methionine synthase MetE, N-terminal / Cobalamin-independent synthase, N-terminal domain / Cobalamin-independent methionine synthase MetE, C-terminal/archaeal / Cobalamin-independent synthase, Catalytic domain / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / NITRATE ION / 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 Å
AuthorsWheatley, R.W. / Ng, K.K. / Kapoor, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Arch.Biochem.Biophys. / Year: 2015
Title: Fungal cobalamin-independent methionine synthase: Insights from the model organism, Neurospora crassa.
Authors: Wheatley, R.W. / Ng, K.K. / Kapoor, M.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobalamin-Independent Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,53512
Polymers86,4311
Non-polymers1,10511
Water14,646813
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-40 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.045, 95.198, 115.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cobalamin-Independent Methionine synthase


Mass: 86430.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)
References: UniProt: Q8X1E4, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase

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Non-polymers , 5 types, 824 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% w/v PEG3350, 200 mM potassium nitrate, 1 mM TCEP, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.5498 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 7, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 1.88→39.02 Å / Num. all: 494614 / Num. obs: 494614 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 21.54 Å2 / Rmerge(I) obs: 0.122 / Net I/av σ(I): 0.122 / Net I/σ(I): 11.7
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimless0.5.7data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→39.02 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 6698 5.01 %RANDOM
Rwork0.1567 ---
obs0.159 133724 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.35 Å2
Refinement stepCycle: LAST / Resolution: 1.88→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 34 813 6936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086294
X-RAY DIFFRACTIONf_angle_d1.0238504
X-RAY DIFFRACTIONf_dihedral_angle_d13.1472349
X-RAY DIFFRACTIONf_chiral_restr0.04939
X-RAY DIFFRACTIONf_plane_restr0.0051105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90140.28771920.24564138X-RAY DIFFRACTION96
1.9014-1.92370.26812080.21894140X-RAY DIFFRACTION97
1.9237-1.94720.31332310.21554198X-RAY DIFFRACTION97
1.9472-1.97180.24692260.21614107X-RAY DIFFRACTION98
1.9718-1.99780.23632040.20114247X-RAY DIFFRACTION98
1.9978-2.02520.24361990.21254238X-RAY DIFFRACTION99
2.0252-2.05410.26112580.21784221X-RAY DIFFRACTION99
2.0541-2.08470.26072030.21864226X-RAY DIFFRACTION99
2.0847-2.11730.24522130.18794243X-RAY DIFFRACTION99
2.1173-2.1520.22912050.17854223X-RAY DIFFRACTION100
2.152-2.18910.2342460.17784259X-RAY DIFFRACTION99
2.1891-2.22890.2382380.17354253X-RAY DIFFRACTION99
2.2289-2.27180.2412410.17224213X-RAY DIFFRACTION99
2.2718-2.31820.25062060.17594255X-RAY DIFFRACTION100
2.3182-2.36860.22672470.17534237X-RAY DIFFRACTION99
2.3686-2.42370.23222080.17594223X-RAY DIFFRACTION100
2.4237-2.48430.2392260.16534292X-RAY DIFFRACTION100
2.4843-2.55140.18611830.16574255X-RAY DIFFRACTION100
2.5514-2.62650.20042220.15824288X-RAY DIFFRACTION100
2.6265-2.71120.20682360.14764236X-RAY DIFFRACTION100
2.7112-2.80810.20321910.15264359X-RAY DIFFRACTION100
2.8081-2.92050.18362600.1544127X-RAY DIFFRACTION99
2.9205-3.05340.20892230.15124272X-RAY DIFFRACTION99
3.0534-3.21430.17832430.14564222X-RAY DIFFRACTION100
3.2143-3.41560.18292800.13834255X-RAY DIFFRACTION100
3.4156-3.67910.18262580.13574227X-RAY DIFFRACTION100
3.6791-4.0490.1752060.12634254X-RAY DIFFRACTION100
4.049-4.63410.13271830.11444302X-RAY DIFFRACTION99
4.6341-5.83530.17862300.12934264X-RAY DIFFRACTION100
5.8353-39.03090.1762320.15294252X-RAY DIFFRACTION100

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