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- PDB-7qpe: Crystal structure of serine hydroxymethyltransferase, isoform 6 f... -

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Basic information

Entry
Database: PDB / ID: 7qpe
TitleCrystal structure of serine hydroxymethyltransferase, isoform 6 from Arabidopsis thaliana (SHM6)
ComponentsSerine hydroxymethyltransferase 6
KeywordsTRANSFERASE / one-carbon metabolism / tetrahydrofolate
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / pyridoxal phosphate binding / one-carbon metabolic process ...glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / pyridoxal phosphate binding / one-carbon metabolic process / zinc ion binding / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
NITRATE ION / Serine hydroxymethyltransferase 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsRuszkowski, M. / Grzechowiak, M. / Sekula, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant Physiol Biochem. / Year: 2022
Title: Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives.
Authors: Nogues, I. / Sekula, B. / Angelaccio, S. / Grzechowiak, M. / Tramonti, A. / Contestabile, R. / Ruszkowski, M.
History
DepositionJan 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase 6
B: Serine hydroxymethyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4353
Polymers106,3732
Non-polymers621
Water2,288127
1
A: Serine hydroxymethyltransferase 6
B: Serine hydroxymethyltransferase 6
hetero molecules

A: Serine hydroxymethyltransferase 6
B: Serine hydroxymethyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,8716
Polymers212,7474
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area21910 Å2
ΔGint-95 kcal/mol
Surface area61150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.683, 129.683, 302.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11B-667-

HOH

21B-669-

HOH

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Components

#1: Protein Serine hydroxymethyltransferase 6 / AtSHMT6 / Glycine hydroxymethyltransferase 6 / Serine methylase 6


Mass: 53186.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM6, SHMT6, At1g22020, F2E2.7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9LM59, glycine hydroxymethyltransferase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.18 M Ammonium nitrate, 0.09 M Sodium cacodylate 5.3, 20% v/v PEG Smear Low, 10% Ethylene glycol (based on the D1 condition of the BCS screen, Molecular Dimensions). Cryoprotection was ...Details: 0.18 M Ammonium nitrate, 0.09 M Sodium cacodylate 5.3, 20% v/v PEG Smear Low, 10% Ethylene glycol (based on the D1 condition of the BCS screen, Molecular Dimensions). Cryoprotection was obtained by increasing the ethylene glycol concentration to 20 % in the drop with crystals.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→105.28 Å / Num. obs: 49107 / % possible obs: 62 % / Redundancy: 38.5 % / Biso Wilson estimate: 56.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
7.23-105.2833.10.03195.524540.99999.9
2.18-2.4334.42.182.224560.82511.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PZZ

7pzz


Resolution: 2.18→63.4 Å / SU ML: 0.2068 / Cross valid method: FREE R-VALUE / Phase error: 38.803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 981 2 %
Rwork0.2076 48062 -
obs0.2081 49043 61.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.76 Å2
Refinement stepCycle: LAST / Resolution: 2.18→63.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 4 127 6851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796873
X-RAY DIFFRACTIONf_angle_d0.94779273
X-RAY DIFFRACTIONf_chiral_restr0.0508992
X-RAY DIFFRACTIONf_plane_restr0.0071209
X-RAY DIFFRACTIONf_dihedral_angle_d14.94682552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.290.5104120.4218599X-RAY DIFFRACTION5.52
2.29-2.440.3792400.36021968X-RAY DIFFRACTION18.07
2.44-2.620.3312810.29313933X-RAY DIFFRACTION36.02
2.62-2.890.32171580.27927752X-RAY DIFFRACTION70.54
2.89-3.310.25192240.260711018X-RAY DIFFRACTION99.76
3.31-4.170.22662280.193211150X-RAY DIFFRACTION99.86
4.17-63.40.20442380.181411642X-RAY DIFFRACTION99.57
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)
11.61779213750.5719094863590.4179390511192.60444300383-0.829871650131.67150349762-0.0375213735346-0.472930604867-0.2053697058810.2382718807090.198063481049-0.06356285450380.182226409037-0.139937790958-0.1540808791240.348217006980.06515696088540.05723960763170.809176902855-0.0302133656340.32911282586163.235697511-1.73920717492110.456868795
22.765375200720.257792682697-0.9224620773233.28548679290.1329613318554.077590887-0.0961108518314-0.1845414915380.272880742008-0.3648135952420.225401028550.181775103422-0.472223106079-0.0420223565724-0.1054646787380.362659158804-0.123545899448-0.07780666491370.4164720309710.02496379655160.27436930839358.020786137116.791602749385.8364574777
32.277340052530.8449202234950.2709083430943.10526684964-0.00613784577811.26200295491-0.117163719265-0.1773640744560.1513496399040.09503515563290.195486753967-0.00387024523431-0.134294218431-0.00363327247998-0.06171642775010.448400127717-0.0583351437149-0.005945563326170.651414754364-0.1258489674710.31786806302568.609137073821.0548542461101.088695728
41.916489343330.06668227250560.2191759382042.038158729580.2934763737651.38584171387-0.175227093850.383382072578-0.168273781637-0.3832745135510.0623698014005-0.005213154079190.1044801215130.03985958157150.09866927524370.38153309055-0.2745404591550.04408991455220.4459010867170.03612877120770.21327011630366.44358214-1.7587395946628.6397398493
51.373469250660.7365117716350.07490930981673.19165802123-0.4457491930843.00759423372-0.03078158725080.009796915018270.1762863450980.478602134546-0.05898397978580.191350763937-0.375994475550.01211396917990.08401517251070.535774805618-0.25953305575-0.07787279274730.3608137416460.007986143840220.37353765635971.544126847916.797184407153.2800396746
61.55652427064-0.006124903530850.0491630230292.898579003680.1080298314042.43361428492-0.1705920318020.1050767412140.2174694917760.005755035404560.01396908040380.0282993556227-0.353864469245-0.0119852755620.1263022843470.393467931366-0.243808500841-0.07286253098030.2966230038510.04967034280280.24610127995666.273837108117.935385022341.2545322458
72.68370523343-0.438046815844-0.8321129121532.426127735210.7982929544163.43718016437-0.008177598085220.3568383263390.706613998049-0.561020294106-0.1011061885810.423588838913-0.792137233172-0.561513780410.2362365947730.631092899461-0.154036057274-0.2610109125250.5020758094130.1116672051540.49930034997652.20672684926.401555913432.4650033284
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 124 through 220 )AA124 - 2201 - 97
22chain 'A' and (resid 221 through 381 )AA221 - 38198 - 243
33chain 'A' and (resid 382 through 598 )AA382 - 598244 - 429
44chain 'B' and (resid 124 through 220 )BB124 - 2201 - 97
55chain 'B' and (resid 221 through 381 )BB221 - 38198 - 243
66chain 'B' and (resid 382 through 509 )BB382 - 509244 - 358
77chain 'B' and (resid 510 through 598 )BB510 - 598359 - 429

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