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- PDB-6aph: Crystal structure of Adenosylhomocysteinase from Elizabethkingia ... -

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Basic information

Entry
Database: PDB / ID: 6aph
TitleCrystal structure of Adenosylhomocysteinase from Elizabethkingia anophelis NUHP1 in complex with NAD and Adenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Elizabethkingia anophelis / Adenosylhomocysteinase / ahcY / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / one-carbon metabolic process / cytoplasm
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 / Adenosylhomocysteinase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Adenosylhomocysteinase from Elizabethkingia anophelis NUHP1 in complex with NAD and Adenosine
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5434
Polymers49,4941
Non-polymers1,0493
Water7,566420
1
A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,17216
Polymers197,9774
Non-polymers4,19512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area28940 Å2
ΔGint-106 kcal/mol
Surface area50500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.590, 132.590, 102.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

21A-744-

HOH

31A-952-

HOH

41A-997-

HOH

51A-1012-

HOH

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Components

#1: Protein Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 49494.133 Da / Num. of mol.: 1 / Fragment: ElanA.00032.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: ahcY, BD94_1936 / Plasmid: ElanA.00032.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A077EDS4, adenosylhomocysteinase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: RigakuReagents screen JCSG+ b5 (40% MPD, 5% PEG8000, 100 mM sodium cacodylate / HCl, pH 6.5), 20 mg/mL ElanA.00032.a.B1.PS38147 + 2 mM magnesium chloride + 2 mM ATP (added by mistake due to ...Details: RigakuReagents screen JCSG+ b5 (40% MPD, 5% PEG8000, 100 mM sodium cacodylate / HCl, pH 6.5), 20 mg/mL ElanA.00032.a.B1.PS38147 + 2 mM magnesium chloride + 2 mM ATP (added by mistake due to sample mix-up), cryoprotection: direct, puck: GLC4-2, for phasing, a crystal from the same well was incubated in 10% ethylene glycol + 5 M potassium iodide (final concentration 500 mM), data collected in-house

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDAug 4, 2016
RIGAKU SATURN 944+2CCDAug 4, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond[111]SINGLE WAVELENGTHMx-ray1
2Diamond[111]SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.65→43.4 Å / Num. obs: 63783 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.984 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.057 / Χ2: 1.028 / Net I/σ(I): 24.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.6911.0160.474.6646890.940.49399.9
1.69-1.7410.9960.3655.9545460.9630.383100
1.74-1.7911.0610.2987.2844420.9760.31299.9
1.79-1.8411.050.2239.7143140.9850.23499.9
1.84-1.9111.0520.17212.3341770.9910.18199.8
1.91-1.9711.0610.13715.2440650.9940.14499.9
1.97-2.0511.0950.11418.5639070.9960.1299.7
2.05-2.1311.0770.09322.4637480.9970.09799.6
2.13-2.2211.0540.0826.0536210.9980.08399.6
2.22-2.3311.0850.06929.6234570.9980.07399.3
2.33-2.4611.0770.06332.7732820.9980.06699.2
2.46-2.6111.040.05735.9231270.9990.05999.3
2.61-2.7911.0210.05239.4829280.9990.05498.7
2.79-3.0110.9540.04743.0627310.9990.04998.8
3.01-3.310.9210.04246.7225260.9990.04498.3
3.3-3.6910.8160.03950.4222930.9990.04198
3.69-4.2610.7360.03652.3120290.9990.03897.7
4.26-5.2210.6640.03453.2817340.9990.03697.2
5.22-7.3810.570.03452.0613690.9990.03696.2
7.38-509.5050.03451.547980.9990.03692.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PHENIXrefinement
ARPmodel building
Cootmodel building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.65→43.4 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.8
RfactorNum. reflection% reflection
Rfree0.1695 2017 3.16 %
Rwork0.1476 --
obs0.1483 63773 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.41 Å2 / Biso mean: 29.7084 Å2 / Biso min: 11.31 Å2
Refinement stepCycle: final / Resolution: 1.65→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 71 427 3807
Biso mean--19.58 37.41 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093546
X-RAY DIFFRACTIONf_angle_d1.0374854
X-RAY DIFFRACTIONf_chiral_restr0.069555
X-RAY DIFFRACTIONf_plane_restr0.007660
X-RAY DIFFRACTIONf_dihedral_angle_d15.7732156
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 (%)
1.65-1.69130.26891620.204443514513100
1.6913-1.7370.22281450.195843744519100
1.737-1.78810.22121600.180543584518100
1.7881-1.84580.17481380.164943984536100
1.8458-1.91180.17221450.152143604505100
1.9118-1.98840.17591520.146943654517100
1.9884-2.07890.18271370.155143944531100
2.0789-2.18850.18391220.151444204542100
2.1885-2.32560.18591490.149344014550100
2.3256-2.50510.14521450.14544412455799
2.5051-2.75720.17961270.15144414454199
2.7572-3.1560.15741520.14394434458699
3.156-3.97580.16181300.13344456458698
3.9758-43.41530.15111530.13974619477297
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)
11.2972-0.10690.9712.5535-0.26762.3901-0.1025-0.4781-0.19580.4681-0.0420.08590.23970.04250.02080.25050.01760.05390.36140.10660.2156-36.494336.181512.3412
21.0625-0.03790.4911.06290.51071.4882-0.0792-0.4118-0.27620.4120.1334-0.20740.3890.5049-0.04690.36310.0986-0.05590.50750.12420.3291-20.769933.140310.019
30.7307-0.0584-0.20740.61310.24440.866-0.0088-0.14890.02920.07650.0422-0.0820.01030.0374-0.030.0889-0.0074-0.02720.1643-0.0060.1203-17.558357.7327-2.0067
41.0298-0.0402-0.33710.7650.52681.7995-0.0242-0.1612-0.25560.11070.0631-0.05890.30930.2076-0.05070.17860.0081-0.00980.15310.04440.2255-30.572828.1637-10.3901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 45 )A6 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 194 )A46 - 194
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 359 )A195 - 359
4X-RAY DIFFRACTION4chain 'A' and (resid 360 through 437 )A360 - 437

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