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- PDB-1a7a: STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DE... -

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Basic information

Entry
Database: PDB / ID: 1a7a
TitleSTRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH
ComponentsS-ADENOSYLHOMOCYSTEINE HYDROLASE
KeywordsHYDROLASE / NAD BINDING PROTEIN
Function / homology
Function and homology information


Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / Methylation / melanosome / one-carbon metabolic process / endoplasmic reticulum ...Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / Methylation / melanosome / one-carbon metabolic process / endoplasmic reticulum / extracellular exosome / nucleus / 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
Chem-ADC / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 2.8 Å
AuthorsTurner, M.A. / Yuan, C.-S. / Borchardt, R.T. / Hershfield, M.S. / Smith, G.D. / Howell, P.L.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.
Authors: Turner, M.A. / Yuan, C.S. / Borchardt, R.T. / Hershfield, M.S. / Smith, G.D. / Howell, P.L.
History
DepositionMar 10, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: S-ADENOSYLHOMOCYSTEINE HYDROLASE
B: S-ADENOSYLHOMOCYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8386
Polymers97,0452
Non-polymers1,7934
Water82946
1
A: S-ADENOSYLHOMOCYSTEINE HYDROLASE
B: S-ADENOSYLHOMOCYSTEINE HYDROLASE
hetero molecules

A: S-ADENOSYLHOMOCYSTEINE HYDROLASE
B: S-ADENOSYLHOMOCYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,67612
Polymers194,0894
Non-polymers3,5878
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area28230 Å2
ΔGint-119 kcal/mol
Surface area52310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.930, 168.020, 137.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.972, -0.234, -0.005), (-0.234, 0.972, -0.009), (0.007, -0.008, -1)
Vector: 55.241, 6.822, 70.193)

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Components

#1: Protein S-ADENOSYLHOMOCYSTEINE HYDROLASE


Mass: 48522.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE DERIVATIZED PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P23526, adenosylhomocysteinase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ADC / (1'R,2'S)-9-(2-HYDROXY-3'-KETO-CYCLOPENTEN-1-YL)ADENINE


Mass: 233.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95
DetectorType: BRANDEIS / Detector: CCD / Date: Jul 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 50613 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 350530
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
SHAKE-N-BAKE2model building
CNS0.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHAKE-N-BAKEV. 2.0phasing
RefinementMethod to determine structure: SAS / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 5838962.45 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4804 9.7 %RANDOM
Rwork0.227 ---
obs0.227 49460 97.5 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--21.44 Å20 Å20 Å2
2--13.55 Å20 Å2
3---7.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 122 46 6834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.891.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it1.312
X-RAY DIFFRACTIONc_scangle_it1.992.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 751 9.3 %
Rwork0.311 7294 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWAT_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor obs: 0.311

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