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- PDB-5v96: Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Nae... -

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Basic information

Entry
Database: PDB / ID: 5v96
TitleCrystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine
ComponentsS-adenosyl-l-homocysteine Hydrolase
KeywordsHYDROLASE / SSGCID / Naegleria fowleri / s-adenosyl-l-homocysteine hydrolase / NAD / adenosine / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / nucleotide binding / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Adenosylhomocysteinase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 23, 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

Downloads & links

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Assembly

Deposited unit
A: S-adenosyl-l-homocysteine Hydrolase
B: S-adenosyl-l-homocysteine Hydrolase
C: S-adenosyl-l-homocysteine Hydrolase
D: S-adenosyl-l-homocysteine Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,32862
Polymers211,3704
Non-polymers6,95858
Water30,6071699
1
A: S-adenosyl-l-homocysteine Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,48914
Polymers52,8431
Non-polymers1,64613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-adenosyl-l-homocysteine Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,67517
Polymers52,8431
Non-polymers1,83316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: S-adenosyl-l-homocysteine Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,55115
Polymers52,8431
Non-polymers1,70814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: S-adenosyl-l-homocysteine Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,61316
Polymers52,8431
Non-polymers1,77015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37000 Å2
ΔGint-44 kcal/mol
Surface area57270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.830, 134.330, 239.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
S-adenosyl-l-homocysteine Hydrolase


Mass: 52842.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: AmoebaDB with Gene ID NF0035640
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Gene: NF0035640 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1Z0YU84*PLUS

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Non-polymers , 5 types, 1757 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1699 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: NafoA.00032.a.B1.PW37932 at 19.8 mg/ml incubated with 3 mM each SAH and NAD, then mixed 1:1 with an equal volume JCSG+(c4): 10% (w/v) PEG-6000, 0.1 M HEPES free acid/NaOH, pH = 7.0, ...Details: NafoA.00032.a.B1.PW37932 at 19.8 mg/ml incubated with 3 mM each SAH and NAD, then mixed 1:1 with an equal volume JCSG+(c4): 10% (w/v) PEG-6000, 0.1 M HEPES free acid/NaOH, pH = 7.0, cryoprotected with 20% ethylene glycol

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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: Feb 24, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→48.408 Å / Num. obs: 152740 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.244 % / Biso Wilson estimate: 19.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.101 / Χ2: 1.014 / Net I/σ(I): 16.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.056.2860.4983.89111970.9030.543100
2.05-2.116.2790.3964.84108950.9410.432100
2.11-2.176.2910.3285.86106140.9590.357100
2.17-2.246.2950.2846.76102910.9680.30999.9
2.24-2.316.210.2577.6599910.970.28199.9
2.31-2.396.2970.218.996900.980.229100
2.39-2.486.2980.18410.1493690.9840.201100
2.48-2.586.2920.15911.6489980.9880.173100
2.58-2.76.2880.13513.3486650.9920.148100
2.7-2.836.2950.11715.2582450.9930.128100
2.83-2.986.2850.09817.8579100.9950.107100
2.98-3.166.260.0821.0174780.9960.08899.9
3.16-3.386.2570.06525.170270.9970.07199.9
3.38-3.656.2190.05230.1465650.9980.05799.9
3.65-46.1650.04633.0960600.9980.0599.9
4-4.476.1810.03937.3855070.9990.04399.9
4.47-5.166.1480.03738.1149070.9990.04199.9
5.16-6.326.0910.04234.1441830.9980.04699.8
6.32-8.945.9910.03537.9732700.9990.03999.7
8.94-48.4085.510.03142.4818780.9980.03498.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OND

3ond


Resolution: 2→48.408 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.41
RfactorNum. reflection% reflection
Rfree0.1797 1977 1.29 %
Rwork0.1383 --
obs0.1388 152736 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.55 Å2 / Biso mean: 22.5332 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 2→48.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14187 0 484 1716 16387
Biso mean--29.2 33.44 -
Num. residues----1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715161
X-RAY DIFFRACTIONf_angle_d0.86820544
X-RAY DIFFRACTIONf_chiral_restr0.0552369
X-RAY DIFFRACTIONf_plane_restr0.0052681
X-RAY DIFFRACTIONf_dihedral_angle_d14.3079145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.20691290.16271063410763
2.05-2.10550.20811330.14911068510818
2.1055-2.16740.19671700.1431063910809
2.1674-2.23740.19511350.14321066010795
2.2374-2.31730.18511360.15091068410820
2.3173-2.41010.20831410.13861070610847
2.4101-2.51980.19091350.1411068610821
2.5198-2.65260.20171280.13871072810856
2.6526-2.81880.18761430.14381072310866
2.8188-3.03640.1711420.14861080110943
3.0364-3.34190.17761420.14551078110923
3.3419-3.82530.17641490.13031082510974
3.8253-4.81880.14591320.11121094311075
4.8188-48.42170.17041620.1451126411426
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)
10.0795-0.09980.01180.3431-0.26840.5981-0.0093-0.0099-0.0655-0.12090.02210.00470.1409-0.0082-0.01760.17420.00620.02270.14640.0170.167416.1808-17.588930.5271
20.74590.07430.19360.89340.04751.4726-0.03020.01190.0211-0.11030.0043-0.0287-0.0520.07070.02480.13220.00420.03840.13250.03570.097529.609712.71922.5474
30.36740.09270.18290.4718-0.43033.5105-0.0516-0.0194-0.0898-0.18510.02260.05090.4296-0.15940.01220.2497-0.01660.03810.12870.01380.18523.7017-4.9304-3.1209
40.71650.0029-0.22120.8884-0.19710.71140.00930.09810.0024-0.0790.0260.15450.0287-0.1061-0.03660.11260.0025-0.01380.1280.01940.10317.90385.034716.093
50.3478-0.08870.12140.5868-0.39651.5421-0.06310.0005-0.0273-0.0556-0.0907-0.08960.10780.31980.14280.13590.05920.0530.21680.05620.202637.7101-4.004725.8922
61.13990.6805-0.27772.897-0.61962.0074-0.00260.1207-0.0643-0.364-0.0242-0.02930.0214-0.06810.03930.18590.0278-0.01260.1633-0.01480.1074-2.168832.707712.0256
70.72970.1642-0.04861.23370.08390.6284-0.0301-0.0102-0.005-0.13820.01460.0697-0.0591-0.04690.00560.1330.0196-0.00510.12020.02340.0902-3.657439.42122.2858
80.53260.673-0.09273.7713-0.35160.4008-0.0295-0.0884-0.01180.10150.0043-0.1043-0.09860.04140.03150.14520.0268-0.0030.1706-0.01790.08153.011749.051534.8714
90.5855-0.17960.0450.4896-0.06130.7320.0290.02270.0338-0.0111-0.0119-0.0766-0.04530.1335-0.02480.1005-0.01590.01920.1170.02180.107418.595327.706631.9559
100.36890.4401-0.06861.8341-0.90210.6905-0.0821-0.084-0.0230.09650.23890.2944-0.0595-0.1117-0.14960.10780.04820.04190.20210.05640.1804-11.394621.697844.2268
112.05492.2417-0.76664.967-3.25224.07220.016-0.281-0.37290.0711-0.1606-0.30460.11330.29440.16630.14730.0259-0.0080.19540.03790.191216.55750.428973.2584
121.0620.1058-0.50221.1569-0.06380.77060.0433-0.0564-0.06060.1074-0.05060.0187-0.03680.05440.00740.1465-0.01660.00340.12880.02350.08482.959310.098975.4102
131.61630.215-1.55461.0063-0.21552.74180.02220.06250.0240.05830.01750.1162-0.079-0.0958-0.05790.1120.0148-0.00350.10250.01850.1173-6.714715.230472.1901
140.2984-0.03420.09150.66430.00210.6780.03330.0003-0.06530.02290.01110.0880.0637-0.0556-0.04420.09840.00050.02520.150.04260.1539-1.35790.899851.2923
151.29240.9616-1.3960.8328-1.16582.44480.1557-0.10140.03660.2143-0.11010.0102-0.32990.1646-0.05650.1863-0.02-0.00330.1383-0.01490.105913.051530.146455.2747
160.97090.16880.21320.87630.21921.09880.0028-0.1181-0.07020.1084-0.02040.01530.1304-0.06180.01460.17940.01650.03290.14540.0470.174417.5446-28.363449.7225
172.1187-1.18020.80231.6555-0.44431.165500.0303-0.0552-0.0489-0.0185-0.2110.14670.17140.02030.1490.03760.04210.13690.0340.199435.3423-28.847942.0529
180.95630.0841-0.13320.8393-0.09541.24610.0153-0.1239-0.02130.0732-0.034-0.1082-0.00640.1803-0.00120.09150.0170.00070.17540.04230.136229.7296-0.38248.7696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 377 through 472 )C377 - 472
2X-RAY DIFFRACTION2chain 'D' and (resid 8 through 138 )D8 - 138
3X-RAY DIFFRACTION3chain 'D' and (resid 139 through 230 )D139 - 230
4X-RAY DIFFRACTION4chain 'D' and (resid 231 through 416 )D231 - 416
5X-RAY DIFFRACTION5chain 'D' and (resid 417 through 472 )D417 - 472
6X-RAY DIFFRACTION6chain 'A' and (resid 6 through 32 )A6 - 32
7X-RAY DIFFRACTION7chain 'A' and (resid 33 through 138 )A33 - 138
8X-RAY DIFFRACTION8chain 'A' and (resid 139 through 230 )A139 - 230
9X-RAY DIFFRACTION9chain 'A' and (resid 231 through 416 )A231 - 416
10X-RAY DIFFRACTION10chain 'A' and (resid 417 through 472 )A417 - 472
11X-RAY DIFFRACTION11chain 'B' and (resid 9 through 32 )B9 - 32
12X-RAY DIFFRACTION12chain 'B' and (resid 33 through 163 )B33 - 163
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 230 )B164 - 230
14X-RAY DIFFRACTION14chain 'B' and (resid 231 through 416 )B231 - 416
15X-RAY DIFFRACTION15chain 'B' and (resid 417 through 472 )B417 - 472
16X-RAY DIFFRACTION16chain 'C' and (resid 8 through 138 )C8 - 138
17X-RAY DIFFRACTION17chain 'C' and (resid 139 through 230 )C139 - 230
18X-RAY DIFFRACTION18chain 'C' and (resid 231 through 376 )C231 - 376

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