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- PDB-5vmb: Crystal structure of a glycine hydroxymethyltransferase from Acin... -

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Basic information

Entry
Database: PDB / ID: 5vmb
TitleCrystal structure of a glycine hydroxymethyltransferase from Acinetobacter baumannii
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / NIAID / THF / serine production / protein production / essentiallity screen / structural genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from L-serine / tetrahydrofolate interconversion / cobalt ion binding / transaminase activity / folic acid metabolic process / methyltransferase activity ...serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from L-serine / tetrahydrofolate interconversion / cobalt ion binding / transaminase activity / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding / methylation / 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) ...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
Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a glycine hydroxymethyltransferase from Acinetobacter baumannii
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)46,0771
Polymers46,0771
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine hydroxymethyltransferase

A: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)92,1542
Polymers92,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area7420 Å2
ΔGint-48 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.840, 95.840, 109.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Serine hydroxymethyltransferase / Serine methylase


Mass: 46076.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: glyA, glyA2, A7M79_08275, A7M90_04720, A7N09_12635, A8A08_14715, A8G88_00905, AB895_0334, AB988_4249, ABUW_1333, APD06_10955, AZE33_14190, BGC29_02480, IX87_07645, LV38_04033
Production host: Escherichia coli (E. coli)
References: UniProt: V5VBJ2, glycine hydroxymethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: AcbaC.00008.a.B1.PW37629 at 18.5 mg/mL with 3 mM glycine, 3 mM ADP, 2 mM MgCl2 against Morpheus screen condition E5 10% PEG 10,000, 20% PEG 550 MME, 30 mM each diethyleneglycol, ...Details: AcbaC.00008.a.B1.PW37629 at 18.5 mg/mL with 3 mM glycine, 3 mM ADP, 2 mM MgCl2 against Morpheus screen condition E5 10% PEG 10,000, 20% PEG 550 MME, 30 mM each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol, 0.1 M MOPS/Hepes pH 7.5, crystal tracking ID 261070e5, unique puck ID eob8-7

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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: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→38.815 Å / Num. obs: 19797 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.492 % / Biso Wilson estimate: 68.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.04 / Χ2: 0.976 / Net I/σ(I): 25.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.575.5140.5932.5714660.8490.657100
2.57-2.645.5710.4523.4414260.9050.5100
2.64-2.715.5510.3474.4913770.9340.384100
2.71-2.85.550.2396.2113560.9690.264100
2.8-2.895.5680.1748.2512990.9840.192100
2.89-2.995.5230.13110.4312770.9910.145100
2.99-3.15.5650.09214.8112240.9940.101100
3.1-3.235.5870.07817.711530.9960.08699.9
3.23-3.375.5410.05423.3811300.9990.06100
3.37-3.545.5410.04329.6810860.9990.047100
3.54-3.735.5330.03438.0710260.9990.03799.8
3.73-3.955.5080.02944.449690.9990.03199.9
3.95-4.235.5180.02750.559050.9990.02999.9
4.23-4.565.4510.02653.348470.9990.02899.8
4.56-55.4370.02557.0978910.02799.9
5-5.595.4010.02457.797060.9990.02699.9
5.59-6.465.4620.02359.346340.9990.026100
6.46-7.915.310.0265.045360.9990.022100
7.91-11.184.7740.0264.113980.9990.02395.7
11.18-38.8154.0470.01856.421930.9990.02179.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p3m

4p3m


Resolution: 2.5→38.815 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.02
RfactorNum. reflection% reflection
Rfree0.2332 1959 9.92 %
Rwork0.1815 --
obs0.1867 19746 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.34 Å2 / Biso mean: 94.7445 Å2 / Biso min: 49.07 Å2
Refinement stepCycle: final / Resolution: 2.5→38.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 0 22 2970
Biso mean---72.04 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073009
X-RAY DIFFRACTIONf_angle_d0.8744106
X-RAY DIFFRACTIONf_chiral_restr0.05466
X-RAY DIFFRACTIONf_plane_restr0.006548
X-RAY DIFFRACTIONf_dihedral_angle_d15.8461770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.56260.32571180.286313011419100
2.5626-2.63190.30321480.261312541402100
2.6319-2.70930.29051510.249212541405100
2.7093-2.79670.34681330.249312831416100
2.7967-2.89660.32741490.244512531402100
2.8966-3.01260.29811620.235112521414100
3.0126-3.14960.32381540.227912451399100
3.1496-3.31560.29091450.234512861431100
3.3156-3.52320.24281100.205212931403100
3.5232-3.7950.21951450.175112561401100
3.795-4.17650.20851370.164212971434100
4.1765-4.77990.1941470.14812631410100
4.7799-6.01860.23531340.166612971431100
6.0186-38.81950.18641260.14891253137995
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)
11.50681.437-0.03988.17620.85584.08680.0878-0.218-0.2667-0.9702-0.0019-0.87910.0980.66-0.12830.58430.1770.1070.9560.02930.629835.192741.0637-17.6536
21.87390.80760.14477.5392-1.68524.50110.6438-0.67340.04590.7292-0.84530.3301-0.2004-0.07720.12710.4052-0.04740.02460.9655-0.01710.571919.301940.8541-6.4053
31.8231-0.1943-0.24986.6003-2.12136.79370.3839-0.86420.23661.4487-0.38080.5375-0.4682-0.5617-0.08750.6636-0.23610.13811.3412-0.14960.72511.079439.47175.5174
41.443-0.0845-0.30144.9124-1.53651.75520.3899-1.0716-0.29381.3826-0.4750.5133-0.0126-0.21570.06290.8506-0.34330.08191.56820.08240.753210.869427.944210.8652
51.35260.35350.61125.7613-0.87422.72270.4844-0.4176-0.47-0.2602-0.35030.30340.8504-0.7096-0.13940.6592-0.1504-0.15690.94530.14440.629719.116616.4357-3.83
63.5322-0.83551.98775.3841-2.0358.33180.3509-0.1602-0.5605-0.4363-0.2274-0.42281.2090.0248-0.0880.6355-0.0075-0.1520.49080.16670.701628.060812.5327-6.9079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 26 )A-2 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 67 )A27 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 118 )A68 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 264 )A119 - 264
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 339 )A265 - 339
6X-RAY DIFFRACTION6chain 'A' and (resid 340 through 417 )A340 - 417

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