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- PDB-4otl: X-ray Crystal Structure of Serine Hydroxymethyl Transferase from ... -

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Basic information

Entry
Database: PDB / ID: 4otl
TitleX-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia bound to PLP and Glycine
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / serine hydroxymethyl transferase
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: X-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia bound to PLP and Glycine
Authors: Fairman, J.W. / Jensen, M.M. / Sullivan, A.H. / Edwards, T.E. / Lorimer, D.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,28413
Polymers183,9334
Non-polymers1,3519
Water14,232790
1
A: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6116
Polymers91,9662
Non-polymers6444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-44 kcal/mol
Surface area26140 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6737
Polymers91,9662
Non-polymers7065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-45 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.970, 179.690, 75.510
Angle α, β, γ (deg.)90.00, 115.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid
41chain D and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
311chain C and segidC0
411chain D and segidD0

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Components

#1: Protein
Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 45983.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: glyA, BCAL3197 / Production host: Escherichia coli (E. coli)
References: UniProt: B4ECY9, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG1 condition G7: 0.1 M TRIS pH 8.50, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→89.85 Å / Num. all: 108579 / Num. obs: 107615 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.305 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.18
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.050.4562.96199
2.05-2.110.43.31199
2.11-2.170.3144.18199.2
2.17-2.240.2594.92199
2.24-2.310.2235.65199.1
2.31-2.390.2036.22199.2
2.39-2.480.1737.07199.3
2.48-2.580.1567.83199.4
2.58-2.70.1329.19199.3
2.7-2.830.11610.24199.5
2.83-2.980.10211.46199.4
2.98-3.160.09112.71199.3
3.16-3.380.08213.8199.3
3.38-3.650.07415.28199
3.65-40.06916.36198.8
4-4.470.06416.97198.7
4.47-5.160.06117.48199.2
5.16-6.320.05517.43199.1
6.32-8.940.05318.22198.7
8.940.05318.48195.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXdev_1659refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N0W
Resolution: 2→42.559 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 23.34 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflection
Rfree0.2236 5376 5 %
Rwork0.1798 --
obs0.182 107598 99.31 %
all-108579 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.999 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20.96 Å2
2---1.38 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2→42.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12336 0 84 790 13210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412870
X-RAY DIFFRACTIONf_angle_d0.90717519
X-RAY DIFFRACTIONf_dihedral_angle_d11.4234708
X-RAY DIFFRACTIONf_chiral_restr0.0351953
X-RAY DIFFRACTIONf_plane_restr0.0042336
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7436X-RAY DIFFRACTION5.01TORSIONAL
12B7436X-RAY DIFFRACTION5.01TORSIONAL
13C7436X-RAY DIFFRACTION5.01TORSIONAL
14D7436X-RAY DIFFRACTION5.01TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.02270.31381840.24323390X-RAY DIFFRACTION99
2.0227-2.04640.29391520.2293407X-RAY DIFFRACTION99
2.0464-2.07140.28251820.22863406X-RAY DIFFRACTION99
2.0714-2.09760.33171760.21953412X-RAY DIFFRACTION99
2.0976-2.12520.25631610.21673394X-RAY DIFFRACTION99
2.1252-2.15430.27462000.20593386X-RAY DIFFRACTION99
2.1543-2.18510.27531680.20353412X-RAY DIFFRACTION99
2.1851-2.21770.23361760.19433399X-RAY DIFFRACTION99
2.2177-2.25240.25681740.19173377X-RAY DIFFRACTION99
2.2524-2.28930.2151580.18783436X-RAY DIFFRACTION99
2.2893-2.32880.24731750.19173385X-RAY DIFFRACTION99
2.3288-2.37110.26581720.19153412X-RAY DIFFRACTION99
2.3711-2.41670.24852070.1913364X-RAY DIFFRACTION99
2.4167-2.4660.25851790.18553461X-RAY DIFFRACTION99
2.466-2.51970.25661670.19413387X-RAY DIFFRACTION100
2.5197-2.57830.22261850.19333403X-RAY DIFFRACTION99
2.5783-2.64270.24141890.19323401X-RAY DIFFRACTION100
2.6427-2.71420.22541730.18223418X-RAY DIFFRACTION100
2.7142-2.7940.24511880.18773431X-RAY DIFFRACTION100
2.794-2.88420.22971720.1913397X-RAY DIFFRACTION100
2.8842-2.98730.21841830.19273402X-RAY DIFFRACTION100
2.9873-3.10680.24781940.19343400X-RAY DIFFRACTION99
3.1068-3.24820.25531770.20053443X-RAY DIFFRACTION100
3.2482-3.41940.21641910.19573385X-RAY DIFFRACTION99
3.4194-3.63350.19851910.17963398X-RAY DIFFRACTION99
3.6335-3.91380.20531670.16543438X-RAY DIFFRACTION99
3.9138-4.30740.19331760.15083402X-RAY DIFFRACTION99
4.3074-4.92990.19751760.14343411X-RAY DIFFRACTION99
4.9299-6.2080.18511920.1533452X-RAY DIFFRACTION99
6.208-42.56870.15941910.1383413X-RAY DIFFRACTION98
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)
10.12280.210.23360.77240.25170.6738-0.0117-0.03830.06750.0901-0.00130.0302-0.18020.436-0.00450.2334-0.08530.00370.27870.01530.25221.3993-26.2448-32.2637
21.186-0.27860.10970.94170.05121.03520.1350.21640.1367-0.2236-0.08820.0086-0.0357-0.10410.01730.0990.0048-0.03650.18380.03920.2581-18.1246-39.3312-41.7565
30.74-0.0373-0.07310.48380.19070.88980.0310.0621-0.01880.0707-0.04850.22120.0407-0.1407-0.03180.0898-0.0102-0.00850.1510.00580.2698-24.4392-38.2029-32.1031
40.87420.4874-0.0931.40550.42390.88240.1567-0.1430.21160.2597-0.07590.2355-0.17610.0657-0.05050.3519-0.08540.09230.1773-0.0150.2264-14.9803-20.5032-15.6903
50.5671-0.2836-1.06920.47650.47753.38550.29410.31370.1719-0.34750.03560.1185-0.20130.041-0.08980.21010.0148-0.07730.29340.02110.26910.822626.4658-47.4305
60.10620.02530.0680.3819-0.04940.3969-0.05740.09590.0503-0.08260.02750.09620.0605-0.05410.03070.2191-0.0392-0.00240.15960.00470.19728.959323.7843-35.9671
70.8220.0781-0.26811.3457-0.38981.3606-0.09370.02880.0029-0.34560.0365-0.24380.0780.34230.07140.1666-0.0176-0.01060.197-0.02170.203227.889616.7904-34.56
80.70760.0599-0.20380.77540.1820.1732-0.1374-0.1173-0.20240.1465-0.0203-0.00830.45350.13750.12410.45360.00310.05470.17880.04310.273812.7595-2.86-22.1526
90.95250.1092-0.61940.9005-0.07561.2332-0.0437-0.1047-0.01810.08720.0099-0.09530.0820.180.0130.1618-0.0185-0.03010.148-0.01540.154920.444112.4715-25.402
101.82440.8585-0.32761.6662-0.04520.76050.2601-0.3080.49110.4538-0.05850.3004-0.07070.226-0.0290.2354-0.03840.02120.1825-0.04950.17561.474422.2829-15.9192
110.69130.0138-0.25780.8357-0.03270.6947-0.07180.139-0.01780.04020.00410.26880.3149-0.19570.04210.2571-0.08660.02370.1896-0.0180.2342-7.43238.9952-22.7183
120.67310.53140.05111.2985-0.43830.2664-0.12030.0396-0.1348-0.1320.02120.22060.3091-0.08580.07960.2818-0.06920.04760.1844-0.01410.2645-3.580510.2953-25.2015
131.04990.544-0.11930.3216-0.2280.63030.10590.14250.17510.01710.08510.50920.0448-0.37450.0930.1448-0.0362-0.02760.26260.02740.349-13.02122.7955-26.3785
140.1042-0.07350.01020.08950.02970.05350.032-0.0286-0.01440.04940.0836-0.0937-0.00190.15540.4431-0.06380.1131-0.04420.37740.0690.31615.8747-44.7531-35.4734
151.01080.1014-0.18710.9198-0.30331.47820.11580.00820.15560.0052-0.02440.0575-0.44080.1125-0.08330.2343-0.05440.01030.18670.04420.2307-5.1216-24.1184-45.2384
160.76020.09210.04410.72160.22161.24850.00130.23130.1595-0.33580.02450.1183-0.259-0.0335-0.01650.3132-0.0109-0.03350.24040.09040.2338-11.6952-26.7861-60.9277
171.1575-0.06610.11421.54540.29851.2835-0.00080.195-0.0109-0.31210.1134-0.10570.02360.4499-0.06860.2472-0.01760.06680.37460.01760.21246.2458-45.412-65.3114
181.15750.2475-0.52581.1653-0.09082.22880.14770.05550.3604-0.1240.05010.1845-0.6161-0.1375-0.01680.3373-0.05650.00810.1710.00490.3220.463734.6741-38.2168
190.1678-0.0859-0.15310.3396-0.01670.51780.0368-0.04520.1008-0.20740.0264-0.1426-0.11820.1802-0.03230.3075-0.04370.04490.227-0.00770.240919.480124.7436-49.75
201.12790.0158-0.31590.67690.37880.9244-0.09850.1887-0.1947-0.0531-0.05250.07910.3097-0.2450.06140.2348-0.0522-0.04330.2474-0.03490.22512.46711.9242-47.6051
210.3531-0.1406-0.24610.61110.26030.2511-0.16220.179-0.246-0.28440.0071-0.10440.45250.06470.03230.58110.02840.11710.2838-0.06480.319725.884-0.9265-55.5458
220.9535-0.4062-0.17480.5090.29630.5489-0.04130.2435-0.1424-0.1588-0.03140.11090.3316-0.06420.06450.3397-0.0318-0.01090.2273-0.0510.178713.61819.3333-53.5914
230.71790.3069-0.33531.08310.32211.05740.02840.1701-0.0442-0.15910.0926-0.23020.02730.2861-0.09810.5017-0.00380.10350.3808-0.01820.215237.129818.648-61.7342
240.2191-0.1972-0.43810.21030.37081.35410.13360.27880.3269-0.28230.0516-0.2841-0.36910.42410.02360.7199-0.13460.21040.41810.00250.362440.053332.3629-60.1133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 279 )
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 415 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 29 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 54 )
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 110 )
8X-RAY DIFFRACTION8chain 'B' and (resid 111 through 183 )
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 279 )
10X-RAY DIFFRACTION10chain 'B' and (resid 280 through 302 )
11X-RAY DIFFRACTION11chain 'B' and (resid 303 through 347 )
12X-RAY DIFFRACTION12chain 'B' and (resid 348 through 373 )
13X-RAY DIFFRACTION13chain 'B' and (resid 374 through 415 )
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 29 )
15X-RAY DIFFRACTION15chain 'C' and (resid 30 through 110 )
16X-RAY DIFFRACTION16chain 'C' and (resid 111 through 279 )
17X-RAY DIFFRACTION17chain 'C' and (resid 280 through 415 )
18X-RAY DIFFRACTION18chain 'D' and (resid 0 through 29 )
19X-RAY DIFFRACTION19chain 'D' and (resid 30 through 54 )
20X-RAY DIFFRACTION20chain 'D' and (resid 55 through 87 )
21X-RAY DIFFRACTION21chain 'D' and (resid 88 through 210 )
22X-RAY DIFFRACTION22chain 'D' and (resid 211 through 279 )
23X-RAY DIFFRACTION23chain 'D' and (resid 280 through 373 )
24X-RAY DIFFRACTION24chain 'D' and (resid 374 through 415 )

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