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- PDB-4ot8: X-ray Crystal Structure of Serine Hydroxymethyl Transferase from ... -

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Basic information

Entry
Database: PDB / ID: 4ot8
TitleX-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia bound to PLP and Serine
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 / tetrahydrofolate interconversion / pyridoxal phosphate 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 / 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
PYRIDOXAL-5'-PHOSPHATE / SERINE / 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 Serine
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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)185,34212
Polymers183,9334
Non-polymers1,4098
Water16,087893
1
A: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6716
Polymers91,9662
Non-polymers7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-49 kcal/mol
Surface area26060 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6716
Polymers91,9662
Non-polymers7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-43 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.220, 179.840, 75.640
Angle α, β, γ (deg.)90.00, 115.25, 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 / Pyridoxal phosphate


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


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 893 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 condition F2: 0.2 M ammonium acetate, 0.1 M BIS-TRIS pH 6.50, 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: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→89.92 Å / Num. all: 107749 / Num. obs: 98253 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.381 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.29
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.050.6371.71194.7
2.05-2.110.5422.06194.5
2.11-2.170.4252.57194.1
2.17-2.240.3243.29193.8
2.24-2.310.2823.78193.5
2.31-2.390.2474.36192.9
2.39-2.480.2085192.5
2.48-2.580.1775.79192
2.58-2.70.1437.18191.9
2.7-2.830.1178.53190.6
2.83-2.980.110.03190.2
2.98-3.160.08111.75189.2
3.16-3.380.0713.84189.1
3.38-3.650.05816.53187.6
3.65-40.0518.65187.3
4-4.470.04719.66186.9
4.47-5.160.04420.25186.6
5.16-6.320.04419.93186
6.32-8.940.03922.11184
8.940.03324.29178.7

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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 4MSO
Resolution: 2→42.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 21.97 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflection
Rfree0.2063 4895 4.98 %
Rwork0.1654 --
obs0.1675 98244 91.38 %
all-107749 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20.82 Å2
2---0.78 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12290 0 88 893 13271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512768
X-RAY DIFFRACTIONf_angle_d117386
X-RAY DIFFRACTIONf_dihedral_angle_d13.2184632
X-RAY DIFFRACTIONf_chiral_restr0.0391951
X-RAY DIFFRACTIONf_plane_restr0.0052314
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7471X-RAY DIFFRACTION3.115TORSIONAL
12B7471X-RAY DIFFRACTION3.115TORSIONAL
13C7471X-RAY DIFFRACTION3.115TORSIONAL
14D7471X-RAY DIFFRACTION3.115TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.02270.30341680.25253188X-RAY DIFFRACTION95
2.0227-2.04640.31241950.24283185X-RAY DIFFRACTION95
2.0464-2.07140.30211720.23873230X-RAY DIFFRACTION94
2.0714-2.09760.28181820.23453207X-RAY DIFFRACTION95
2.0976-2.12520.27821910.2273181X-RAY DIFFRACTION94
2.1252-2.15430.26591450.21333203X-RAY DIFFRACTION94
2.1543-2.18510.27211800.20853202X-RAY DIFFRACTION94
2.1851-2.21770.24661430.19663212X-RAY DIFFRACTION94
2.2177-2.25240.2471770.19053204X-RAY DIFFRACTION94
2.2524-2.28930.24851690.19083171X-RAY DIFFRACTION93
2.2893-2.32880.24091730.18833159X-RAY DIFFRACTION94
2.3288-2.37110.2561580.18283190X-RAY DIFFRACTION93
2.3711-2.41670.24461470.18393146X-RAY DIFFRACTION93
2.4167-2.4660.22451880.17773143X-RAY DIFFRACTION92
2.466-2.51970.2381460.17873177X-RAY DIFFRACTION93
2.5197-2.57830.23931440.17093119X-RAY DIFFRACTION92
2.5783-2.64270.22481630.16863156X-RAY DIFFRACTION92
2.6427-2.71420.20011520.16463125X-RAY DIFFRACTION92
2.7142-2.7940.21271620.16653108X-RAY DIFFRACTION90
2.794-2.88420.22291660.1693060X-RAY DIFFRACTION90
2.8842-2.98730.24151560.16913081X-RAY DIFFRACTION91
2.9873-3.10680.21621750.17153053X-RAY DIFFRACTION90
3.1068-3.24820.21551740.16973018X-RAY DIFFRACTION89
3.2482-3.41940.17831510.16753043X-RAY DIFFRACTION89
3.4194-3.63350.19841400.15133021X-RAY DIFFRACTION88
3.6335-3.91380.16361610.1412979X-RAY DIFFRACTION87
3.9138-4.30740.1721540.12972970X-RAY DIFFRACTION88
4.3074-4.92980.13941630.12922980X-RAY DIFFRACTION87
4.9298-6.20790.17341520.14142962X-RAY DIFFRACTION86
6.2079-42.37920.13771480.13162876X-RAY DIFFRACTION83
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)
10.1029-0.1932-0.01460.57070.19460.13370.06150.23510.1563-0.1771-0.0713-0.0465-0.0720.11410.04640.1560.0179-0.07140.27850.03390.23593.249330.6351-48.5422
20.5010.089-0.26860.46610.01210.7452-0.0737-0.0578-0.1211-0.0619-0.0301-0.08880.19770.1508-0.09430.1594-0.0031-0.00910.10610.01350.139417.825211.7509-26.7952
30.0998-0.0285-0.14820.4187-0.14090.5183-0.0263-0.00740.01570.03270.05170.11640.1002-0.08730.02850.1053-0.0519-0.01620.1166-0.0040.15230.86618.6693-25.0377
40.01040.01510.03870.04920.00370.08710.071-0.0380.15710.03110.0322-0.0192-0.13720.23590.00120.1538-0.04680.01530.2111-0.00320.2021.7283-23.5576-32.7152
50.3722-0.0229-0.01580.0905-0.03970.10920.05080.2320.0075-0.0305-0.0354-0.00760.0507-0.02840.0010.10130.0161-0.02680.12710.02410.1479-12.5993-42.2291-42.6076
60.03330.0345-0.0230.0447-0.04450.06170.1216-0.050.1183-0.0143-0.0605-0.041-0.055-0.00150.02690.1760.0629-0.05190.35220.05860.4232-30.1384-25.0687-39.7084
70.10810.09620.00920.1358-0.01040.02380.01660.01770.09580.0884-0.11160.2792-0.0364-0.2448-0.02670.08440.01220.00050.2598-0.01750.3606-36.0308-28.9056-28.6113
80.1627-0.0865-0.0540.22250.11350.19870.02320.0693-0.00290.0603-0.02320.08960.0823-0.0459-0.02610.0915-0.0088-0.01640.09140.01530.1518-19.9585-38.1397-33.6021
90.15680.05870.22970.0693-0.01380.54890.1525-0.15420.03250.1135-0.03920.05130.11370.12430.19730.2249-0.07060.04810.12540.00730.1264-14.4391-29.8457-12.3449
100.1160.0885-0.06010.14580.02110.15230.0629-0.08440.12440.14520.02190.1668-0.13180.05170.00120.2296-0.03380.05350.1124-0.00380.1879-15.0462-14.8048-16.2341
110.25780.15360.18240.3467-0.01120.69220.0226-0.09820.1328-0.01850.00640.2147-0.0305-0.1782-0.00950.1956-0.11220.03090.154-0.03430.29921.006137.3479-38.0683
120.00940.00580.00360.02740.00890.01490.04820.06180.0097-0.1919-0.0249-0.0922-0.05120.12660.00070.1903-0.0210.02240.19730.01230.13319.909427.5216-49.6962
130.13630.1117-0.14930.1366-0.13370.2243-0.12350.1629-0.1233-0.24680.01020.06450.3696-0.0512-0.04280.32360.01830.00560.1651-0.04460.165114.7277.9618-47.937
140.06990.02690.04720.02770.0250.0411-0.10080.1276-0.175-0.00310.0084-0.02240.1580.0933-0.05380.62110.12850.2350.2129-0.05560.194231.64-0.9576-61.0696
150.19470.03590.06050.0153-0.00440.1161-0.08280.3314-0.2239-0.443-0.04020.08810.4179-0.1137-0.10610.4948-0.02340.02950.0265-0.269-0.141916.13059.6053-55.8655
160.00140.00120.0010.0005-0.00850.0217-0.02510.14180.022-0.07080.02340.064-0.02460.06640.00330.60490.04550.17190.39240.0364-0.004128.428724.477-69.0763
170.1055-0.04710.10750.57440.3760.55190.01630.06770.0119-0.00490.016-0.16550.1580.26180.24830.45820.04390.08890.30740.02220.172840.764819.8909-58.9459
180.00320.0036-0.0040.00260.0015-0.00230.04190.03980.107-0.0604-0.0144-0.0624-0.03890.16790.03150.4543-0.05840.25120.3340.04320.231940.973834.8198-60.0464
190.04520.02880.02630.0615-0.0180.0618-0.0065-0.0166-0.0061-0.010.0259-0.15770.05880.2625-0.00170.10780.0361-0.01690.19070.01930.16934.4255-38.0075-42.2958
200.0239-0.01670.01710.0143-0.00210.01350.031-0.07710.19750.04270.00990.1134-0.097-0.0056-00.2421-0.04940.01120.19570.03280.2699-6.2282-14.0019-40.8271
210.18660.0127-0.0080.06160.09240.13670.05710.2340.0412-0.20780.04860.1714-0.0726-0.13980.11780.2255-0.0081-0.07110.27120.0970.2415-18.2405-26.889-57.0156
220.03080.01340.00160.09560.02720.0126-0.00880.22230.0386-0.280.02070.0854-0.1962-0.077-0.02560.31240.0107-0.08540.33730.11350.1882-16.0078-27.389-72.3438
230.3089-0.1345-0.20560.38360.15640.55080.09110.03290.3741-0.26410.0678-0.0278-0.34960.02330.19510.22280.00560.0020.17370.10950.2086-7.9737-20.1989-56.427
240.0917-0.0221-0.01440.00640.00140.00350.03340.07020.1376-0.10210.0319-0.0677-0.01280.0230.02980.2221-0.07230.04950.31040.04190.165910.1001-30.766-66.7034
250.1059-0.1451-0.01070.1858-0.00620.0140.0440.0919-0.0299-0.18830.05120.15380.06580.0910.00030.2194-0.0319-0.01570.26360.03480.1641-0.5951-43.6323-67.4104
260.0381-0.03470.04330.0308-0.01850.07770.03790.1235-0.0874-0.10870.0988-0.09960.06910.23580.01370.22490.03660.0140.41-0.01940.211812.5202-48.7162-62.6268
270.01920.0199-0.02160.0028-0.0130.00730.02380.0256-0.04820.03390.04940.05640.0040.025100.25120.0122-0.02230.22840.04720.22990.5587-12.4355-45.0686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 415 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 54 )
5X-RAY DIFFRACTION5chain 'B' and (resid 55 through 110 )
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 141 )
7X-RAY DIFFRACTION7chain 'B' and (resid 142 through 183 )
8X-RAY DIFFRACTION8chain 'B' and (resid 184 through 279 )
9X-RAY DIFFRACTION9chain 'B' and (resid 280 through 302 )
10X-RAY DIFFRACTION10chain 'B' and (resid 303 through 415 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 29 )
12X-RAY DIFFRACTION12chain 'C' and (resid 30 through 54 )
13X-RAY DIFFRACTION13chain 'C' and (resid 55 through 141 )
14X-RAY DIFFRACTION14chain 'C' and (resid 142 through 183 )
15X-RAY DIFFRACTION15chain 'C' and (resid 184 through 279 )
16X-RAY DIFFRACTION16chain 'C' and (resid 280 through 302 )
17X-RAY DIFFRACTION17chain 'C' and (resid 303 through 373 )
18X-RAY DIFFRACTION18chain 'C' and (resid 374 through 414 )
19X-RAY DIFFRACTION19chain 'D' and (resid 7 through 54 )
20X-RAY DIFFRACTION20chain 'D' and (resid 55 through 87 )
21X-RAY DIFFRACTION21chain 'D' and (resid 88 through 141 )
22X-RAY DIFFRACTION22chain 'D' and (resid 142 through 183 )
23X-RAY DIFFRACTION23chain 'D' and (resid 184 through 279 )
24X-RAY DIFFRACTION24chain 'D' and (resid 280 through 302 )
25X-RAY DIFFRACTION25chain 'D' and (resid 303 through 373 )
26X-RAY DIFFRACTION26chain 'D' and (resid 374 through 414 )
27X-RAY DIFFRACTION27chain 'E' and (resid 501 through 801 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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