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- PDB-5tls: 2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from C... -

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Basic information

Entry
Database: PDB / ID: 5tls
Title2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with DZ2002 and NAD
ComponentsAdenosylhomocysteinase
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Chem-ZD2 / Adenosylhomocysteinase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: 2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with DZ2002 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
DepositionOct 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 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
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)230,23932
Polymers224,8034
Non-polymers5,43728
Water18,6641036
1
A: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules

B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,23932
Polymers224,8034
Non-polymers5,43728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area16180 Å2
ΔGint-146 kcal/mol
Surface area82420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.520, 133.027, 174.860
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 (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 , 6 types, 1064 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-ZD2 / (2S)-4-(6-amino-9H-purin-9-yl)-2-hydroxybutanoic acid


Mass: 237.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C9H11N5O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM ZD2002, 1mM NAD; 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: Jun 2, 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: 2.4→30 Å / Num. obs: 109137 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.892 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HM8

5hm8


Resolution: 2.4→29.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 11.727 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 5445 5 %RANDOM
Rwork0.14993 ---
obs0.15178 102888 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.872 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å20 Å20 Å2
2--2.85 Å20 Å2
3----5.99 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15619 0 342 1036 16997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916388
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215808
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.99722173
X-RAY DIFFRACTIONr_angle_other_deg0.913336515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.56952009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35525.194695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.587153071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8921572
X-RAY DIFFRACTIONr_chiral_restr0.0920.22504
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0218133
X-RAY DIFFRACTIONr_gen_planes_other0.0190.023491
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_it1.5343.377997
X-RAY DIFFRACTIONr_mcbond_other1.5343.377996
X-RAY DIFFRACTIONr_mcangle_it2.6235.04910019
X-RAY DIFFRACTIONr_mcangle_other2.6235.04910020
X-RAY DIFFRACTIONr_scbond_it1.7053.6488391
X-RAY DIFFRACTIONr_scbond_other1.6463.628323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7595.32912053
X-RAY DIFFRACTIONr_long_range_B_refined5.52340.36919024
X-RAY DIFFRACTIONr_long_range_B_other5.43339.9618782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 389 -
Rwork0.233 7515 -
obs--99.95 %
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)
11.7252-0.26210.31380.91440.13080.99230.0038-0.04920.07510.1380.0057-0.1331-0.10660.0749-0.00950.1351-0.03770.00180.0197-0.03070.1629-2.32879.651353.1406
20.230.12170.20960.53860.31090.78530.01360.0339-0.00980.06650.0361-0.14350.00520.1363-0.04970.0188-0.00510.00020.0257-0.01090.13240.3907-6.507441.5037
31.31990.64071.20030.90170.28751.59840.1579-0.22880.05380.2358-0.16470.1832-0.0928-0.20380.00680.1522-0.01110.07820.1219-0.03440.1763-27.429-5.850748.6809
42.4364-0.42090.22131.1355-0.22831.46590.0828-0.1168-0.33710.00450.03110.33160.3921-0.3037-0.11390.1656-0.10080.01230.08040.05310.267-37.2813-41.491338.6938
50.5553-0.0920.02410.8383-0.23791.05610.0029-0.0899-0.03970.02210.02290.19080.0955-0.2181-0.02580.0152-0.02390.01950.0630.00840.1416-37.4823-21.692931.9717
61.96120.7103-0.44140.6325-0.4740.470.0342-0.3029-0.0520.0957-0.0487-0.12640.08470.05930.01450.35730.0258-0.04540.24030.00960.3073-14.3826-28.560848.4916
71.1976-0.6473-0.18661.6380.24851.31830.04920.0943-0.1034-0.1950.01230.10980.1302-0.092-0.06150.0848-0.0121-0.05450.01660.00190.1104-33.4646-29.0047-11.1581
80.4452-0.08780.27560.38170.03770.91350.05120.0426-0.0413-0.0590.0063-0.00150.11980.071-0.05750.09890.016100.00810.00140.1196-17.5637-28.59560.637
90.466-0.20630.0441.49891.29931.42-0.07090.07110.1819-0.27880.0350.0176-0.2848-0.05160.03590.2114-0.0134-0.01740.09760.07950.159-23.1666-1.4795-6.8784
100.9373-0.48640.09891.90830.46611.2714-0.0632-0.0460.1685-0.08960.1778-0.3926-0.23240.5461-0.11460.2019-0.17590.09090.3066-0.03280.321912.98699.69868.2464
110.7507-0.0658-0.06410.91220.38971.470.02080.19130.264-0.39090.0504-0.1303-0.56580.2753-0.07110.4096-0.15130.08410.12980.07140.25130.090218.0169-2.4139
120.6642-0.0539-0.04910.61710.35051.0140.01540.06590.1398-0.13890.0038-0.0348-0.25310.1098-0.01920.1512-0.04820.03630.03380.03020.1534-9.45194.0078.6963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 175
2X-RAY DIFFRACTION2A176 - 436
3X-RAY DIFFRACTION3A437 - 495
4X-RAY DIFFRACTION4B1 - 175
5X-RAY DIFFRACTION5B176 - 429
6X-RAY DIFFRACTION6B430 - 495
7X-RAY DIFFRACTION7C3 - 175
8X-RAY DIFFRACTION8C176 - 436
9X-RAY DIFFRACTION9C437 - 495
10X-RAY DIFFRACTION10D3 - 119
11X-RAY DIFFRACTION11D120 - 265
12X-RAY DIFFRACTION12D266 - 495

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