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- PDB-5t8k: 1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from ... -

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Basic information

Entry
Database: PDB / ID: 5t8k
Title1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine and NAD
Components(Adenosylhomocysteinase) x 2
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
ADENINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Adenosylhomocysteinase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine and NAD.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,32529
Polymers224,8794
Non-polymers5,44725
Water34,6791925
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32920 Å2
ΔGint-145 kcal/mol
Surface area68610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.686, 182.785, 96.250
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein Adenosylhomocysteinase


Mass: 56200.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC / References: UniProt: Q5CPH1, adenosylhomocysteinase
#2: Protein Adenosylhomocysteinase


Mass: 56276.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC / References: UniProt: Q5CPH1, adenosylhomocysteinase

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Non-polymers , 9 types, 1950 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#6: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1925 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM Adenine, 1mM NAD, 1mM Homocysteine, Screen: Classics II (D9), 0.1M Bis-Tris-HCL (pH 8.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 166729 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 20.8
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2 / CC1/2: 0.65 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-5HM8

5hm8


Resolution: 1.95→29.92 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.705 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17296 8283 5 %RANDOM
Rwork0.14092 ---
obs0.1425 158251 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.47 Å2
2--0.14 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15562 0 364 1925 17851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916863
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216366
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.99322828
X-RAY DIFFRACTIONr_angle_other_deg0.896337874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.17552113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29225.233709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.082153158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1831572
X-RAY DIFFRACTIONr_chiral_restr0.0910.22563
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0218921
X-RAY DIFFRACTIONr_gen_planes_other0.0190.023635
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2732.0978255
X-RAY DIFFRACTIONr_mcbond_other1.2732.0978253
X-RAY DIFFRACTIONr_mcangle_it2.1583.13410433
X-RAY DIFFRACTIONr_mcangle_other2.1573.13410434
X-RAY DIFFRACTIONr_scbond_it1.5882.4258608
X-RAY DIFFRACTIONr_scbond_other1.5882.4258608
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6413.50412396
X-RAY DIFFRACTIONr_long_range_B_refined5.74126.99320262
X-RAY DIFFRACTIONr_long_range_B_other5.47325.88219578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 615 -
Rwork0.231 11653 -
obs--99.99 %
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)
10.7321-0.1259-0.63340.68010.31691.74950.0317-0.2407-0.05650.2076-0.0391-0.02050.03090.14180.00730.161-0.03540.00110.21990.02150.008567.514836.7794214.4989
20.54460.26860.08890.60890.09050.4410.0455-0.1466-0.02430.1728-0.05390.08970.0245-0.05060.00840.1144-0.02140.06130.13660.00260.038249.427832.6464199.2099
30.43920.13750.09160.07860.1822.19880.0319-0.02350.11080.0377-0.03470.0379-0.23040.14480.00280.1254-0.04590.01470.1184-0.01350.072571.905849.7214189.2108
41.6718-0.09660.18211.15060.00190.78210.03010.3404-0.0478-0.3228-0.05960.14860.0595-0.05020.02960.15870.0257-0.04230.1811-0.05850.037438.85819.1186139.4652
50.4011-0.1795-0.08550.49430.03420.51420.03050.0725-0.119-0.0569-0.03160.13020.0895-0.08560.00120.0383-0.0064-0.01110.0793-0.04030.100134.288818.9684158.8145
60.8234-0.30030.00550.3963-0.08560.32240.03470.1168-0.1033-0.0655-0.05440.08730.0747-0.04740.01970.0319-0.0076-0.00110.0461-0.03810.037840.495218.3512157.8596
71.21840.1709-0.4270.9692-0.06831.09-0.01430.18590.1465-0.1134-0.01840.2079-0.0969-0.20590.03280.0450.0459-0.03210.0911-0.00340.073240.241460.447161.8714
81.63330.1564-0.65422.615-0.0812.12850.07610.20360.3315-0.2695-0.0638-0.2022-0.4230.1167-0.01240.149-0.00390.01520.06110.06390.11160.655473.645158.7041
90.4138-0.03610.02640.40540.06850.31520.00010.01320.0657-0.0109-0.03070.0368-0.0409-0.01640.03050.03930.00550.01480.0543-0.00360.028256.172848.1688170.7298
101.8603-0.48070.1591.23340.00040.5357-0.046-0.2808-0.11750.25680.07560.13060.0603-0.063-0.02960.1264-0.01150.05250.09640.06380.085547.1078-3.5412198.4729
110.2712-0.29480.30921.3483-0.13020.42060.11840.0271-0.0989-0.0339-0.01980.07830.14070.0641-0.09860.10510.011-0.0010.05030.02080.113657.4181-12.49185.341
120.6430.09270.05170.4925-0.05740.20460.0361-0.0331-0.1450.0681-0.0405-0.01370.05610.0220.00440.04310.00140.01390.02410.01340.057455.88447.5956180.0962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 204
2X-RAY DIFFRACTION2A205 - 427
3X-RAY DIFFRACTION3A428 - 495
4X-RAY DIFFRACTION4B3 - 174
5X-RAY DIFFRACTION5B175 - 333
6X-RAY DIFFRACTION6B334 - 495
7X-RAY DIFFRACTION7C3 - 119
8X-RAY DIFFRACTION8C120 - 203
9X-RAY DIFFRACTION9C204 - 495
10X-RAY DIFFRACTION10D2 - 119
11X-RAY DIFFRACTION11D120 - 263
12X-RAY DIFFRACTION12D264 - 495

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