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- PDB-5jpi: 2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from ... -

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Basic information

Entry
Database: PDB / ID: 5jpi
Title2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with D-Eritadenine and NAD
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / S-adenosylhomocysteinase / D-Eritadenine / 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
D-ERITADENINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Adenosylhomocysteinase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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: 2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with D-Eritadenine 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 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 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

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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)229,82329
Polymers224,8034
Non-polymers5,02125
Water22,0321223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29920 Å2
ΔGint-162 kcal/mol
Surface area67410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.847, 121.218, 178.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / 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, 1248 molecules

#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: Chemical
ChemComp-DEA / D-ERITADENINE


Mass: 253.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11N5O4 / Comment: inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1223 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.9 MG/ML, 0.5M SODIUM CHLORIDE, 0.1M TRIS HCL (PH 8.3), DEA; Screen: JCSG+ (A11), 0.2M Ammonium phosphate, 0.1M TRIS-HCL (pH 8.5), 50% (v/v) MPD

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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: Apr 14, 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: 2.15→30 Å / Num. obs: 136687 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 32.1 Å2 / CC1/2: 0.887 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 20.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3 / % possible all: 100

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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: 5HM8

5hm8


Resolution: 2.15→29.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 8.386 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18125 6830 5 %RANDOM
Rwork0.14219 ---
obs0.14415 129766 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.237 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2--4.79 Å20 Å2
3----2.96 Å2
Refinement stepCycle: 1 / Resolution: 2.15→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15562 0 330 1223 17115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216022
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.99522325
X-RAY DIFFRACTIONr_angle_other_deg0.911337036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.14352041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7625.187694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.403153108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8281572
X-RAY DIFFRACTIONr_chiral_restr0.0930.22531
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0218357
X-RAY DIFFRACTIONr_gen_planes_other0.0190.023527
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_it1.6692.6388069
X-RAY DIFFRACTIONr_mcbond_other1.6672.6378067
X-RAY DIFFRACTIONr_mcangle_it2.7693.94310141
X-RAY DIFFRACTIONr_mcangle_other2.7693.94310142
X-RAY DIFFRACTIONr_scbond_it2.212.988434
X-RAY DIFFRACTIONr_scbond_other2.212.988434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5574.33312185
X-RAY DIFFRACTIONr_long_range_B_refined6.71222.50120118
X-RAY DIFFRACTIONr_long_range_B_other6.71122.50420119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 499 -
Rwork0.218 9361 -
obs--99.08 %
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)
11.77710.00190.0530.99260.20161.24680.06430.13570.1595-0.1319-0.03270.0901-0.222-0.2449-0.03170.11270.07570.01740.08290.05550.104819.3625-18.804-30.4132
20.5307-0.1518-0.04570.7125-0.08260.60020.05670.0861-0.029-0.0494-0.01350.1119-0.0222-0.1427-0.04320.01330.0164-0.00840.07950.00420.057619.9334-38.9487-24.6276
31.5778-0.6242-0.07380.3618-0.06010.52160.12810.24740.0835-0.1563-0.0734-0.1293-0.1673-0.0919-0.05470.31610.02520.06940.23810.01920.218842.3711-30.5888-41.511
41.65090.1205-0.16330.6739-0.02861.27570.11160.1575-0.1132-0.1089-0.0318-0.14260.14640.1111-0.07980.13420.0433-0.00440.0722-0.070.12455.4671-67.4491-48.1985
50.29200.08370.37680.15220.51210.04260.06270.0213-0.06290.0395-0.12520.02160.0603-0.0820.03390.01670.00920.0596-0.04450.088457.9433-52.426-36.0084
60.7801-0.1615-0.67750.77760.11251.04830.06130.1937-0.0691-0.1829-0.09980.0750.0531-0.13920.03850.09220.0093-0.04290.1103-0.0330.051129.8742-53.7126-42.3085
70.97040.25750.04361.48710.21750.85880.0469-0.16460.11920.14020.01970.1036-0.0155-0.1095-0.06660.0270.0190.03140.07620.00730.062624.2407-33.892418.2639
80.54390.0247-0.14720.32940.14210.67520.0278-0.08260.08470.02290.0501-0.0371-0.00030.025-0.07790.02070.0071-0.00350.0256-0.0180.079640.9002-32.13216.6186
90.41430.0301-0.10540.88420.95961.3787-0.031-0.1729-0.12960.20010.06330.00890.2482-0.0565-0.03230.22420.0102-0.02480.19820.0830.202836.322-60.245912.9689
101.09360.23770.02761.42210.14991.18470.0275-0.048-0.34320.12320.0725-0.14220.42310.1949-0.10.21730.121-0.09870.08-0.0250.273268.3524-76.83791.8443
110.9237-0.12950.3160.43660.01430.87980.0532-0.0232-0.23180.05310.02570.01270.24050.023-0.07880.14730.0159-0.05170.0044-0.00680.146848.5092-69.6313-5.8285
120.7158-0.3045-0.08931.3958-0.05380.4175-0.0414-0.22090.03670.25040.066-0.16780.11870.1252-0.02470.10010.0431-0.07140.1295-0.04780.113259.7165-49.432411.3048
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 175
2X-RAY DIFFRACTION2A176 - 429
3X-RAY DIFFRACTION3A430 - 495
4X-RAY DIFFRACTION4B4 - 175
5X-RAY DIFFRACTION5B176 - 436
6X-RAY DIFFRACTION6B437 - 495
7X-RAY DIFFRACTION7C1 - 168
8X-RAY DIFFRACTION8C169 - 436
9X-RAY DIFFRACTION9C437 - 495
10X-RAY DIFFRACTION10D3 - 200
11X-RAY DIFFRACTION11D201 - 433
12X-RAY DIFFRACTION12D434 - 495

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