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- PDB-5jxw: 2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from ... -

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Basic information

Entry
Database: PDB / ID: 5jxw
Title2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Neplanocin-A and NAD
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / S-adenosylhomocysteinase / Neplanocin-A / NAD / 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
Neplanocin-A / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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: 2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Neplanocin-A 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
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Other
Revision 1.2Sep 27, 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_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 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)229,80921
Polymers224,8034
Non-polymers5,00617
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28530 Å2
ΔGint-142 kcal/mol
Surface area67840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.885, 136.486, 107.805
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Adenosylhomocysteinase


Mass: 56200.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / 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 , 6 types, 771 molecules

#2: Chemical
ChemComp-6OS / Neplanocin-A / (1S,2R,5R)-5-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)cyclopent-3-ene-1,2-diol


Mass: 263.253 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C11H13N5O3
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


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


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3),1mM NeplanocinA; Screen: Classics II (D7), 0.1M Bis-Tris-HCL (pH 6.5), 25% (w/v) PEG 3350

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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 225 mm CCD / Detector: CCD / Date: Apr 18, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 96622 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 41.6 Å2 / CC1/2: 0.87 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 17.1
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-5HM8

5hm8


Resolution: 2.25→29.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 13.603 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.216 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22103 4857 5 %RANDOM
Rwork0.17341 ---
obs0.1758 91403 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.575 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å24.32 Å2
2---2.58 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15383 0 338 754 16475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215621
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.99621760
X-RAY DIFFRACTIONr_angle_other_deg0.893336077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.85251965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1325.206680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.998153006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1691568
X-RAY DIFFRACTIONr_chiral_restr0.0860.22469
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0217750
X-RAY DIFFRACTIONr_gen_planes_other0.0190.023418
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_it1.62.8227851
X-RAY DIFFRACTIONr_mcbond_other1.5992.827847
X-RAY DIFFRACTIONr_mcangle_it2.6674.2239817
X-RAY DIFFRACTIONr_mcangle_other2.6664.2239818
X-RAY DIFFRACTIONr_scbond_it1.7943.1488255
X-RAY DIFFRACTIONr_scbond_other1.7943.1488255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.914.60911944
X-RAY DIFFRACTIONr_long_range_B_refined6.38923.61319130
X-RAY DIFFRACTIONr_long_range_B_other6.3623.32818871
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 384 -
Rwork0.391 6561 -
obs--98.05 %
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)
12.99760.78830.29921.06940.57031.5630.1666-0.1432-0.44520.2944-0.0174-0.16780.24750.2524-0.14920.13880.018-0.12960.22430.03280.2217-26.1822-31.83068.3007
21.8185-0.1325-0.62821.88080.13182.0230.005-0.1071-0.00270.1726-0.02530.27960.1287-0.13660.02030.0381-0.0095-0.01390.1501-0.00550.1605-49.137-23.91529.7112
30.34960.0232-0.39930.87350.31650.60970.05560.04460.0306-0.02970.00850.0249-0.06880.0154-0.0640.0410.0178-0.07080.28960.0050.2025-30.5402-22.8939-15.5885
41.35770.5898-0.09391.54630.57321.35640.05980.0638-0.06280.1165-0.06730.1960.0982-0.20310.00750.0457-0.0035-0.08070.336-0.0010.285-39.7993-37.3491-18.0507
50.66810.5578-0.55380.8621-0.73910.65960.1308-0.06720.1060.147-0.05350.0334-0.12230.0832-0.07730.0799-0.0092-0.06870.2421-0.03920.1707-17.0756-10.3811-1.9178
61.76930.47690.28771.60790.52110.8412-0.10010.21730.243-0.41290.07080.0707-0.2598-0.00710.02940.18220.021-0.03770.17470.08290.0961-20.662411.7333-38.3142
71.5202-0.4261-1.14283.22291.44531.5413-0.1562-0.04020.0457-0.17760.2039-0.2673-0.10090.3228-0.04760.2218-0.0325-0.04250.25690.03160.1418-7.788224.6678-20.6743
80.3194-0.3133-0.11181.47630.03310.32380.03470.00670.0333-0.11610.0195-0.1563-0.09770.0101-0.05410.0524-0.0068-0.01350.201-0.00420.1545-10.4842-7.6525-22.0373
91.9436-0.4844-0.2721.26280.15050.39430.01630.04880.1417-0.16370.0097-0.2956-0.12330.0659-0.0260.0572-0.02770.02680.15090.02340.1457-1.5423-1.4968-29.2008
100.34960.55-0.05542.6117-0.12230.04130.08010.00780.0071-0.0749-0.0210.2798-0.068-0.087-0.05910.21270.1155-0.0220.40620.04690.3089-36.2755-5.668-21.2443
111.1623-0.42520.52010.66740.17432.07160.04090.14570.0986-0.31620.1646-0.2748-0.61830.5618-0.20550.316-0.18130.14340.3598-0.04990.199810.8661-20.0452-56.8816
123.1462-1.2871-0.02362.4231-0.99973.93060.33830.3237-0.0328-0.52890.0007-0.0448-0.12290.0387-0.3390.19260.00880.02740.1639-0.0090.0508-0.6374-29.5415-77.072
130.7381-0.27-0.44830.62510.32141.05010.07320.0455-0.0174-0.21540.0250.0148-0.1726-0.017-0.09820.10760.0191-0.04230.26390.0090.1264-11.6269-29.7098-46.34
142.0676-0.72510.40411.68140.16151.94330.20110.32290.1704-0.343-0.07710.1441-0.5157-0.2279-0.1240.270.1108-0.02110.26270.09260.1193-19.5425-17.2504-55.0375
150.50720.2508-0.20780.5752-0.69922.21790.07170.0321-0.1117-0.06830.0564-0.19040.02160.3148-0.12820.0753-0.0063-0.0250.3943-0.0750.29318.7536-39.2088-40.2328
160.9413-0.6213-0.06141.4790.11881.0008-0.0728-0.0398-0.10050.0941-0.00820.21270.2071-0.0770.0810.0883-0.0133-0.05830.2750.01220.2143-20.1341-65.6917-24.1974
171.8295-0.4874-0.79327.09251.93243.7482-0.1369-0.35260.04450.90950.2602-0.35550.58170.4731-0.12330.18190.0929-0.08880.24750.02810.10532.1753-73.4572-15.5102
180.1695-0.0815-0.21561.63970.40670.88860.0106-0.0358-0.01090.019-0.0063-0.0819-0.01990.0927-0.00430.04090.0282-0.08830.3283-0.00360.207-4.5992-45.0955-22.9306
190.67690.40841.00581.48081.02722.65660.0439-0.043-0.13450.2950.0391-0.00090.11020.0179-0.0830.11930.0043-0.08460.32510.02220.1809-8.5444-48.5092-11.9012
200.276-0.1989-0.07091.4977-0.55490.41620.00850.1021-0.047-0.3671-0.0070.07930.1534-0.043-0.00150.1280.0235-0.07780.321-0.03580.1504-16.3303-49.4328-47.1129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 119
2X-RAY DIFFRACTION2A120 - 204
3X-RAY DIFFRACTION3A205 - 322
4X-RAY DIFFRACTION4A323 - 412
5X-RAY DIFFRACTION5A413 - 495
6X-RAY DIFFRACTION6B3 - 144
7X-RAY DIFFRACTION7B145 - 206
8X-RAY DIFFRACTION8B207 - 333
9X-RAY DIFFRACTION9B334 - 430
10X-RAY DIFFRACTION10B431 - 495
11X-RAY DIFFRACTION11C3 - 147
12X-RAY DIFFRACTION12C148 - 206
13X-RAY DIFFRACTION13C207 - 322
14X-RAY DIFFRACTION14C323 - 412
15X-RAY DIFFRACTION15C413 - 495
16X-RAY DIFFRACTION16D-2 - 157
17X-RAY DIFFRACTION17D158 - 197
18X-RAY DIFFRACTION18D198 - 357
19X-RAY DIFFRACTION19D358 - 426
20X-RAY DIFFRACTION20D427 - 495

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