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- PDB-7qx8: Crystal structure of serine hydroxymethyltransferase, isoform 7 f... -

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Basic information

Entry
Database: PDB / ID: 7qx8
TitleCrystal structure of serine hydroxymethyltransferase, isoform 7 from Arabidopsis thaliana (SHM7)
ComponentsSerine hydroxymethyltransferase 7
KeywordsTRANSFERASE / one-carbon metabolism / tetrahydrofolate
Function / homology
Function and homology information


sulfate ion homeostasis / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / S-adenosylmethionine metabolic process / tetrahydrofolate interconversion / response to cadmium ion / pyridoxal phosphate binding / nucleus / 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
Serine hydroxymethyltransferase 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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 26, 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 7
B: Serine hydroxymethyltransferase 7
C: Serine hydroxymethyltransferase 7
D: Serine hydroxymethyltransferase 7
E: Serine hydroxymethyltransferase 7
F: Serine hydroxymethyltransferase 7
G: Serine hydroxymethyltransferase 7
H: Serine hydroxymethyltransferase 7
I: Serine hydroxymethyltransferase 7
J: Serine hydroxymethyltransferase 7
K: Serine hydroxymethyltransferase 7
L: Serine hydroxymethyltransferase 7


Theoretical massNumber of molelcules
Total (without water)637,88012
Polymers637,88012
Non-polymers00
Water4,612256
1
A: Serine hydroxymethyltransferase 7
B: Serine hydroxymethyltransferase 7
C: Serine hydroxymethyltransferase 7
D: Serine hydroxymethyltransferase 7


Theoretical massNumber of molelcules
Total (without water)212,6274
Polymers212,6274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Serine hydroxymethyltransferase 7
F: Serine hydroxymethyltransferase 7
G: Serine hydroxymethyltransferase 7
H: Serine hydroxymethyltransferase 7


Theoretical massNumber of molelcules
Total (without water)212,6274
Polymers212,6274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Serine hydroxymethyltransferase 7
J: Serine hydroxymethyltransferase 7
K: Serine hydroxymethyltransferase 7
L: Serine hydroxymethyltransferase 7


Theoretical massNumber of molelcules
Total (without water)212,6274
Polymers212,6274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.832, 123.955, 290.536
Angle α, β, γ (deg.)90.000, 93.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Serine hydroxymethyltransferase 7 / AtSHMT7 / Glycine hydroxymethyltransferase 7 / Serine methylase 7


Mass: 53156.672 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM7, SHMT7, At1g36370, F7F23.9
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q84WV0, glycine hydroxymethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 75 mM magnesium chloride, 75 mM sodium citrate tribasic, 0.1 M Bis-Tris pH 6.0, 18 % v/v PEG Smear Broad (based on G8 condition of the BCS screen, Molecular Dimensions). Cryoprotection was ...Details: 75 mM magnesium chloride, 75 mM sodium citrate tribasic, 0.1 M Bis-Tris pH 6.0, 18 % v/v PEG Smear Broad (based on G8 condition of the BCS screen, Molecular Dimensions). Cryoprotection was obtained by supplementation of the original condition with 25% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→58 Å / Num. obs: 121503 / % possible obs: 65.8 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.106 / Net I/σ(I): 10.9
Reflection shellResolution: 2.74→3.07 Å / Redundancy: 4.36 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6069 / CC1/2: 0.841 / Rrim(I) all: 0.627 / % possible all: 65.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7pzz
Resolution: 2.74→58 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 32.758 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1220 1 %RANDOM
Rwork0.1871 ---
obs0.1875 120290 65.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 226.33 Å2 / Biso mean: 76.571 Å2 / Biso min: 14.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å2-0.38 Å2
2---1.24 Å20 Å2
3---2.41 Å2
Refinement stepCycle: final / Resolution: 2.74→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41391 0 0 256 41647
Biso mean---41.13 -
Num. residues----5305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01342290
X-RAY DIFFRACTIONr_bond_other_d0.0040.01540289
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.64557115
X-RAY DIFFRACTIONr_angle_other_deg1.3331.5892847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84455271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71121.7742193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27157372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.49715300
X-RAY DIFFRACTIONr_chiral_restr0.0650.25577
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0247747
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029693
LS refinement shellResolution: 2.74→2.808 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.246 3 -
Rwork0.264 320 -
obs--2.36 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8166-0.29430.27380.87370.00260.50710.0164-0.0576-0.07050.19040.00320.05430.0871-0.0153-0.01960.48130.00960.03340.7411-0.00160.370694.615323.4462102.5954
20.2775-0.3797-0.34531.20030.1870.74860.141-0.0561-0.0459-0.3011-0.21730.0344-0.0888-0.11070.07630.5470.1269-0.0780.6797-0.08010.403489.138933.950675.0099
30.30880.2742-0.09811.09690.36040.83040.1492-0.0614-0.0514-0.2093-0.1983-0.0061-0.0932-0.13960.04910.47330.0908-0.04320.6888-0.02910.404891.608639.043286.9097
41.921-0.1162-1.24041.2598-0.76941.52280.062-0.1206-0.0413-0.0086-0.2829-0.154-0.1282-0.00660.2210.490.0302-0.01120.6717-0.01790.422108.285650.986894.2335
51.0459-0.4099-0.52051.39160.2630.32160.1315-0.1362-0.06060.2265-0.0268-0.0745-0.0526-0.0301-0.10460.4837-0.0005-0.03070.75440.02520.356197.636125.0606102.781
60.242-0.2914-0.06451.3196-0.04391.06850.0811-0.0636-0.1095-0.0575-0.0062-0.05040.17890.1246-0.07480.53430.1147-0.05480.5667-0.01630.5337108.60925.354282.9865
70.86380.2344-0.66451.8892-0.16961.4645-0.0404-0.1087-0.1880.0413-0.01680.27490.2619-0.13220.05720.49980.0146-0.04670.57630.1090.47894.5355-0.084298.2534
81.6181-0.1648-0.22941.562-0.29090.47280.00360.03230.1776-0.4344-0.01310.04360.0577-0.13120.00950.66870.069-0.04230.53470.03250.3731100.58167.602623.5118
90.2653-0.6224-0.32892.0110.39691.2815-0.133-0.130.05070.1360.10570.03840.2201-0.05150.02740.5466-0.00230.02510.61660.00670.430898.2399-5.057452.7361
100.8974-0.7749-0.32140.75940.10931.02230.0060.01790.0682-0.0082-0.06020.06720.1884-0.11970.05410.6065-0.0477-0.0160.5492-0.02690.4123100.6464-7.969139.8762
112.96420.72740.34321.6787-0.33532.59770.1361-0.160.1401-0.0672-0.3104-0.14730.04860.35950.17430.59050.02620.10590.5450.03480.417121.7724-13.30738.1961
126.2606-0.63743.4391.4997-1.36094.68440.25670.18280.7611-0.3627-0.7389-0.43690.34550.52170.48210.4020.01380.23980.60940.12310.4389128.9871-8.805828.9221
130.99090.01-0.27711.89120.41590.28920.09870.07840.2304-0.4842-0.0465-0.13470.1088-0.0099-0.05220.67660.05740.03640.55990.06620.3429104.18815.706723.6617
140.4313-0.37120.16691.4948-0.07651.6672-0.0336-0.09430.3487-0.02930.2043-0.1229-0.0911-0.107-0.17070.51570.01020.05490.3569-0.07710.7591104.071829.706743.9174
150.4532-0.57440.18681.42910.49331.0690.0902-0.04160.124-0.31460.0345-0.0084-0.18640.0275-0.12470.52740.05260.06140.35590.15060.723997.480228.411631.1227
163.90240.34110.19022.48422.09851.824-0.1190.03320.3105-0.5818-0.47920.7231-0.3361-0.33670.59820.63250.2908-0.270.59340.25930.669477.222927.901919.4642
171.73080.72450.01722.07591.01151.3377-0.4355-0.342-0.41060.24530.2139-0.19320.1395-0.04490.22160.5275-0.01360.20040.51560.1160.537236.0965-2.346670.3833
181.766-0.9158-0.82951.4896-0.26121.3589-0.30330.349-0.3081-0.2013-0.028-0.09010.0729-0.45160.33130.5516-0.24970.08230.656-0.23340.379724.74861.972543.057
190.6416-0.8299-0.53812.13020.42231.8149-0.28870.1846-0.1918-0.03510.0533-0.1086-0.1106-0.51520.23530.5097-0.11210.09260.5512-0.05630.43924.596212.097656.8385
201.74910.6414-1.41652.7485-1.33132.4734-0.18620.1271-0.2198-0.01510.0681-0.2033-0.3985-0.31620.11810.6410.016-0.06150.5231-0.05640.383527.156226.941159.5209
211.59053.2514-1.71117.2061-4.33844.554-0.1686-0.0857-0.44060.208-0.2522-0.7436-0.64840.26010.42090.7395-0.0813-0.01180.5828-0.05180.431534.525528.788669.6506
221.9089-0.4991-1.01771.11320.21160.6318-0.3554-0.3272-0.21860.04620.1343-0.09560.06140.08080.22110.57310.02330.09080.5630.0870.494336.86521.252970.9147
231.4151-0.4722-0.7110.84160.15551.3213-0.3317-0.1273-0.263-0.2896-0.0201-0.21710.03170.14240.35190.4380.00540.3820.44380.03190.770957.4179-5.277950.4553
240.7883-0.1995-0.46172.1945-0.25270.9894-0.4652-0.3267-0.3861-0.28360.0589-0.220.29490.20020.40620.50920.24850.46270.26440.33560.896952.9505-24.149167.0023
252.3184-0.36180.98121.4016-0.15750.4292-0.5050.1417-0.74280.05070.69560.4979-0.1480.0994-0.19060.81530.11670.67850.50610.47491.145838.9776-32.056372.8843
260.4273-0.4588-1.1010.49991.17493.0145-0.31030.3883-0.24120.2662-0.43610.20650.5788-0.8350.74640.8336-0.34080.27970.6649-0.2290.6148.6549-9.097-8.9469
271.6053-0.5337-0.17610.2309-0.07482.4844-0.96020.029-0.10640.3524-0.12560.05240.8273-0.02631.08571.4033-0.17550.74230.1975-0.16410.722152.2248-21.388517.5058
281.4306-0.9281-1.93040.64281.14864.1386-0.89730.0505-0.08340.7057-0.10930.08261.21750.39731.00661.2267-0.13240.46530.18560.18680.793366.6907-19.86593.213
292.00890.62651.04370.88121.56152.9524-0.53380.27610.03180.21090.17250.17660.22350.50190.36130.89830.03160.15290.44670.11360.214179.7994-11.7942-0.563
302.2091-0.5023-1.66240.94261.33522.4461-0.04230.3758-0.02310.2658-0.40390.26080.3131-0.55570.44610.8512-0.14260.21350.5113-0.14960.465651.3969-7.1455-9.0979
311.1262-1.0979-0.67821.14090.37332.3403-0.08160.12090.11330.093-0.157-0.0475-0.0851-0.34170.23860.6381-0.09360.19090.332-0.31310.640640.585711.229212.0962
321.1874-1.0173-1.3720.87721.19781.857-0.07030.7418-0.32610.1035-0.65620.32320.0959-0.87530.72650.5516-0.14760.16170.8253-0.4950.751131.44025.1536-2.3897
335.94131.8027-0.17681.2086-0.12030.01430.20150.6015-0.57460.2165-0.20750.3266-0.0264-0.01950.00610.2473-0.21890.09481.3252-0.8630.711516.6083-5.789-11.5704
341.19290.15330.73910.47710.27690.6854-0.062-0.13410.2769-0.1670.01630.00510.1021-0.13590.04560.55830.1032-0.0530.5399-0.02160.474742.904545.120589.1794
350.89390.50670.12990.40310.46821.8894-0.0047-0.2580.1352-0.055-0.04440.00520.0710.08960.04910.45290.0947-0.03990.6945-0.14590.47462.221645.8093111.9349
361.51470.88170.59121.00570.18410.3954-0.11140.09950.4355-0.0624-0.03640.2109-0.04040.09370.14780.51980.0081-0.03590.4960.00180.674465.662264.253894.8814
371.89531.6343-0.82554.80010.91911.2555-0.45770.2250.8629-0.16330.48451.36150.04470.0051-0.02680.75450.1194-0.19510.14660.28740.84455.425276.497987.7133
381.84210.20930.25010.34890.2060.2504-0.1650.15530.3228-0.1760.08940.05280.0122-0.09380.07560.59970.1255-0.1140.5194-0.01450.478543.92448.98289.202
391.80910.21040.14190.26210.41041.1089-0.0609-0.72840.6095-0.1785-0.17290.09390.0136-0.24360.23380.37170.177-0.02680.8786-0.3950.485830.030550.5936113.1236
400.9701-0.35080.04181.4039-0.49541.5518-0.0618-0.3890.1124-0.1968-0.0539-0.08510.3014-0.29810.11570.54520.0309-0.04990.71850.00680.314624.850425.093798.3621
411.29930.07160.6710.9811-0.16941.57140.0913-0.4039-0.24670.0952-0.2276-0.1278-0.0914-0.38880.13630.5701-0.06790.01330.6946-0.10130.267752.881553.6823170.07
422.00160.7154-0.03010.5206-0.58382.03440.21520.0572-0.39690.0838-0.1181-0.03460.1382-0.4983-0.09710.4492-0.188-0.11450.9332-0.40420.519236.114638.8878148.8096
431.9301-0.17940.19290.08930.14810.90360.0723-0.035-0.1311-0.0029-0.1286-0.08140.2705-0.71180.05640.415-0.2018-0.00740.8979-0.23860.450832.159245.8276161.1532
442.2069-0.18430.38432.74971.00870.46570.1439-0.49240.4833-0.1564-0.55060.8242-0.057-0.30350.40670.31390.15430.16071.2425-0.37690.516119.137864.0456169.7204
450.5631-0.0228-0.01310.18180.14551.96650.06-0.3151-0.1077-0.0285-0.3139-0.0057-0.2219-0.38880.25390.5884-0.0158-0.01980.8686-0.13450.345350.068555.9818169.7987
462.38330.28490.11530.24790.41912.50180.08070.2247-0.1588-0.1302-0.31790.0388-0.5711-0.13480.23720.84140.1826-0.06390.6581-0.07310.141961.496863.7668142.828
471.6539-0.16660.68990.2024-0.01852.93980.148-0.0321-0.0784-0.1241-0.31920.0234-0.5440.11360.17120.67610.038-0.04080.563-0.05040.308766.00462.1073154.8816
481.2655-0.40280.35971.9121-0.31612.30480.0729-0.1257-0.107-0.1277-0.2665-0.05890.2550.50080.19370.6044-0.0072-0.09040.68020.16740.319680.505548.0899162.6679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 216
2X-RAY DIFFRACTION2A217 - 377
3X-RAY DIFFRACTION3A378 - 498
4X-RAY DIFFRACTION4A499 - 594
5X-RAY DIFFRACTION5B124 - 216
6X-RAY DIFFRACTION6B217 - 383
7X-RAY DIFFRACTION7B384 - 593
8X-RAY DIFFRACTION8C123 - 216
9X-RAY DIFFRACTION9C217 - 367
10X-RAY DIFFRACTION10C368 - 487
11X-RAY DIFFRACTION11C488 - 555
12X-RAY DIFFRACTION12C556 - 594
13X-RAY DIFFRACTION13D121 - 215
14X-RAY DIFFRACTION14D216 - 377
15X-RAY DIFFRACTION15D378 - 532
16X-RAY DIFFRACTION16D533 - 593
17X-RAY DIFFRACTION17E125 - 216
18X-RAY DIFFRACTION18E217 - 405
19X-RAY DIFFRACTION19E406 - 498
20X-RAY DIFFRACTION20E499 - 557
21X-RAY DIFFRACTION21E561 - 594
22X-RAY DIFFRACTION22F121 - 216
23X-RAY DIFFRACTION23F217 - 423
24X-RAY DIFFRACTION24F424 - 556
25X-RAY DIFFRACTION25F557 - 594
26X-RAY DIFFRACTION26G126 - 216
27X-RAY DIFFRACTION27G217 - 414
28X-RAY DIFFRACTION28G415 - 498
29X-RAY DIFFRACTION29G499 - 593
30X-RAY DIFFRACTION30H124 - 216
31X-RAY DIFFRACTION31H217 - 405
32X-RAY DIFFRACTION32H406 - 532
33X-RAY DIFFRACTION33H533 - 593
34X-RAY DIFFRACTION34I121 - 216
35X-RAY DIFFRACTION35I217 - 423
36X-RAY DIFFRACTION36I424 - 556
37X-RAY DIFFRACTION37I557 - 593
38X-RAY DIFFRACTION38J123 - 216
39X-RAY DIFFRACTION39J217 - 439
40X-RAY DIFFRACTION40J440 - 594
41X-RAY DIFFRACTION41K122 - 216
42X-RAY DIFFRACTION42K217 - 377
43X-RAY DIFFRACTION43K378 - 532
44X-RAY DIFFRACTION44K533 - 593
45X-RAY DIFFRACTION45L124 - 216
46X-RAY DIFFRACTION46L217 - 377
47X-RAY DIFFRACTION47L378 - 498
48X-RAY DIFFRACTION48L499 - 594

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