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- PDB-3gvp: Human SAHH-like domain of human adenosylhomocysteinase 3 -

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Basic information

Entry
Database: PDB / ID: 3gvp
TitleHuman SAHH-like domain of human adenosylhomocysteinase 3
ComponentsAdenosylhomocysteinase 3
KeywordsHYDROLASE / protein co-factor complex / NAD / One-carbon metabolism / Phosphoprotein
Function / homology
Function and homology information


adenosylhomocysteinase / Bicarbonate transporters / S-adenosylmethionine cycle / one-carbon metabolic process / hydrolase activity / neuron projection / endoplasmic reticulum / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSiponen, M.I. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Siponen, M.I. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Schueler, H.
CitationJournal: To be Published
Title: Human S-adenosyl homocysteine hydrolase-like 2 protein crystal structure
Authors: Siponen, M.I. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Siponen, M.I. / Wisniewska, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Schueler, H.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_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: Adenosylhomocysteinase 3
B: Adenosylhomocysteinase 3
C: Adenosylhomocysteinase 3
D: Adenosylhomocysteinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,6348
Polymers193,9804
Non-polymers2,6544
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21100 Å2
ΔGint-107 kcal/mol
Surface area64280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.188, 164.188, 184.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Adenosylhomocysteinase 3 / AdoHcyase 3 / S-adenosyl-L-homocysteine hydrolase 3 / S-adenosylhomocysteine hydrolase-like protein 2


Mass: 48494.969 Da / Num. of mol.: 4 / Fragment: UNP residues 175-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHCYL2, KIAA0828 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96HN2, adenosylhomocysteinase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 12.5% PEG3350, 0.2M sodium malonate, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Mar 1, 2009 / Details: mirrors
RadiationMonochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→19.91 Å / Num. obs: 119253 / % possible obs: 99.9 % / Observed criterion σ(I): 0.102 / Redundancy: 29.6 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 33.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 29.8 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 9 / Num. unique all: 17219 / Rsym value: 0.516 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D64

3d64


Resolution: 2.25→19.91 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.603 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22581 1204 1 %RANDOM
Rwork0.18186 ---
obs0.18231 117967 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refine analyzeLuzzati coordinate error free: 0.177 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13415 0 176 582 14173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213861
X-RAY DIFFRACTIONr_bond_other_d0.0010.029278
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.97418812
X-RAY DIFFRACTIONr_angle_other_deg0.924322723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61251736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61824.547585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.411152419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.461579
X-RAY DIFFRACTIONr_chiral_restr0.0850.22139
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022647
X-RAY DIFFRACTIONr_nbd_refined0.2190.22875
X-RAY DIFFRACTIONr_nbd_other0.1960.29636
X-RAY DIFFRACTIONr_nbtor_refined0.1750.26779
X-RAY DIFFRACTIONr_nbtor_other0.0890.26967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2683
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.26
X-RAY DIFFRACTIONr_mcbond_it0.941.59341
X-RAY DIFFRACTIONr_mcbond_other0.1891.53524
X-RAY DIFFRACTIONr_mcangle_it1.369213848
X-RAY DIFFRACTIONr_scbond_it2.20935821
X-RAY DIFFRACTIONr_scangle_it3.2934.54958
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 95 -
Rwork0.191 8535 -
obs--99.98 %

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