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- PDB-4ccz: Crystal structure of human 5-methyltetrahydrofolate-homocysteine ... -

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Basic information

Entry
Database: PDB / ID: 4ccz
TitleCrystal structure of human 5-methyltetrahydrofolate-homocysteine methyltransferase, the homocysteine and folate binding domains
ComponentsMETHIONINE SYNTHASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


Defective MTRR causes HMAE / Defective MTR causes HMAG / Sulfur amino acid metabolism / cobalamin metabolic process / Cobalamin (Cbl) metabolism / methionine synthase / methionine synthase activity / homocysteine metabolic process / Methylation / methionine biosynthetic process ...Defective MTRR causes HMAE / Defective MTR causes HMAG / Sulfur amino acid metabolism / cobalamin metabolic process / Cobalamin (Cbl) metabolism / methionine synthase / methionine synthase activity / homocysteine metabolic process / Methylation / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / axon regeneration / RHOH GTPase cycle / response to axon injury / cellular response to nitric oxide / nervous system development / methylation / zinc ion binding / cytosol
Similarity search - Function
Homocysteine-binding-like domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain ...Homocysteine-binding-like domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(6S)-5,6,7,8-TETRAHYDROFOLATE / Methionine synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVollmar, M. / Kiyani, W. / Krojer, T. / Goubin, S. / Burgess-Brown, N. / von Delft, F. / Oppermann, U. / Edwards, A. / Arrowsmith, C. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of Human 5-Methyltetrahydrofolate-Homocysteine Methyltransferase, the Homocysteine and Folate Binding Domains
Authors: Vollmar, M. / Kiyani, W. / Krojer, T. / Goubin, S. / Burgess-Brown, N. / von Delft, F. / Oppermann, U. / Edwards, A. / Arrowsmith, C. / Bountra, C. / Yue, W.W.
History
DepositionOct 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: METHIONINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9692
Polymers70,5241
Non-polymers4451
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)166.803, 166.803, 166.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein METHIONINE SYNTHASE / 5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE / VITAMIN-B12 DEPENDENT METHIONINE SYNTHASE / MS


Mass: 70523.828 Da / Num. of mol.: 1 / Fragment: HOMOCYSTEINE AND FOLATE BINDING DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q99707, methionine synthase
#2: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.76 Å3/Da / Density % sol: 55.42 % / Description: NONE
Crystal growDetails: 2.4M SODIUM MALONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→39.32 Å / Num. obs: 21347 / % possible obs: 100 % / Observed criterion σ(I): 2.4 / Redundancy: 13.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q7Q

1q7q


Resolution: 2.7→39.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 32.779 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.687 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27408 1095 5.1 %RANDOM
Rwork0.21705 ---
obs0.22004 20213 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.039 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 32 2 4252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194325
X-RAY DIFFRACTIONr_bond_other_d0.0010.023811
X-RAY DIFFRACTIONr_angle_refined_deg0.911.9685900
X-RAY DIFFRACTIONr_angle_other_deg0.70738668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10924.408152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69715555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2911517
X-RAY DIFFRACTIONr_chiral_restr0.050.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02968
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7314.5172443
X-RAY DIFFRACTIONr_mcbond_other5.73214.5032441
X-RAY DIFFRACTIONr_mcangle_it7.91422.873045
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.37815.5411882
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 71 -
Rwork0.279 1500 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.585-12.87081.729113.0711.69913.4983-0.1014-0.11080.78960.3159-0.2666-0.7069-0.0057-1.72630.36810.7925-0.15110.18441.02260.16140.8629-71.403820.1199-4.7353
24.2733-0.1012-1.28950.19910.69356.2503-0.0220.2013-0.8274-0.1714-0.17090.17180.5526-0.93790.19290.6809-0.0946-0.07050.8554-0.05040.763-65.435316.3311-33.9154
32.0766-0.6122-1.40831.1241-0.55216.40530.0197-0.0914-0.3815-0.28860.21540.27970.4608-0.9506-0.23520.1348-0.0135-0.01740.63360.070.32-63.782723.8949-27.5317
41.69220.32231.23771.52670.54662.61960.08960.1314-0.53610.16960.176-0.01780.3391-0.0657-0.26560.22550.05020.00990.31290.04330.2243-48.891426.5851-9.8098
51.7384-0.2631-0.20951.95531.78266.3039-0.28260.1476-0.00680.12930.09190.5373-0.4815-0.01940.19070.28910.0631-0.01140.22050.05140.2147-47.230344.8793-5.9175
62.852-2.4036-1.262.94270.13332.3578-0.3392-0.13930.22480.46590.6817-0.0067-0.07560.0054-0.34250.3380.0788-0.03330.57870.03740.0719-42.422150.41691.6515
711.17753.0131-5.353936.67835.731625.7994-0.06670.04720.7905-0.24970.6031-0.4982-0.73110.8427-0.53640.3373-0.0234-0.03630.28150.02480.0965-39.404255.897313.7201
81.387-0.2431-0.25193.0491.24151.3688-0.0645-0.0312-0.00250.85510.1931-0.38750.09640.2032-0.12870.56030.0492-0.17460.24070.03760.0855-33.487445.277312.1124
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 33
2X-RAY DIFFRACTION2A34 - 84
3X-RAY DIFFRACTION3A85 - 123
4X-RAY DIFFRACTION4A124 - 457
5X-RAY DIFFRACTION5A458 - 490
6X-RAY DIFFRACTION6A491 - 507
7X-RAY DIFFRACTION7A508 - 512
8X-RAY DIFFRACTION8A513 - 639

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