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- PDB-6gbn: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cyt... -

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Basic information

Entry
Database: PDB / ID: 6gbn
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii in complex with adenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / CELLULAR METHYLATION / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / one-carbon metabolic process / cytoplasm
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
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Adenosylhomocysteinase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsCzyrko, J. / Jaskolski, M. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre (Poland)OPUS 2013/09/B/NZ1/01880 Poland
CitationJournal: Croatica Chemica Acta / Year: 2018
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii, a case of combination of crystallographic and non-crystallographic symmetry.
Authors: Czyrko, J. / Jaskolski, M. / Brzezinski, K.
History
DepositionApr 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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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)196,33418
Polymers192,2194
Non-polymers4,11514
Water13,223734
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,63520
Polymers192,2194
Non-polymers4,41516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area29840 Å2
ΔGint-150 kcal/mol
Surface area53220 Å2
MethodPISA
2
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules

C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,03416
Polymers192,2194
Non-polymers3,81512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area28520 Å2
ΔGint-160 kcal/mol
Surface area53440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.275, 102.445, 188.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

21A-849-

HOH

31B-655-

HOH

41B-881-

HOH

51C-681-

HOH

61D-708-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 48054.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469) (bacteria)
Strain: ATCC 33406 / NCIMB 9469 / Gene: sahH, ahcY, CHU_0610 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus-RIPL / References: UniProt: Q11XG9, adenosylhomocysteinase

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Non-polymers , 6 types, 748 molecules

#2: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 15% (w/v) PEG8000, 0.5 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 110896 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.09→2.21 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LI4

1li4


Resolution: 2.09→48.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.165 / SU ML: 0.154 / SU R Cruickshank DPI: 0.2362 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 2101 1.9 %RANDOM
Rwork0.2103 ---
obs0.2107 108795 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.24 Å2 / Biso mean: 42.602 Å2 / Biso min: 3.47 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20 Å2
2--2.2 Å2-0 Å2
3----4.47 Å2
Refinement stepCycle: final / Resolution: 2.09→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13320 0 276 751 14347
Biso mean--39.77 32.05 -
Num. residues----1732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913982
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213442
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.98218955
X-RAY DIFFRACTIONr_angle_other_deg0.979330985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3151760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60324.786585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.765152470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4481577
X-RAY DIFFRACTIONr_chiral_restr0.0920.22169
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215688
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023021
LS refinement shellResolution: 2.088→2.142 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 152 -
Rwork0.305 7841 -
all-7993 -
obs--98.04 %
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)
11.97270.0236-0.49831.2953-0.04161.68350.01390.4407-0.0344-0.03930.0411-0.3289-0.01220.6067-0.0550.263-0.04980.00770.4451-0.01180.37323.51237.6173-20.0857
21.4489-0.09470.93911.02540.1432.04540.07050.2304-0.1559-0.0286-0.0153-0.09140.21580.2061-0.05520.21360.02120.00330.0393-0.03120.319.5354-14.2402-7.8482
31.0580.3440.19560.80970.34961.44470.01520.07290.14610.06140.0665-0.2654-0.24020.5603-0.08160.2719-0.1358-0.00440.23030.01210.413622.924114.9243-1.0338
41.6223-0.23060.34631.44190.20731.77480.0925-0.10110.0725-0.0475-0.0455-0.2343-0.24170.3285-0.0470.3694-0.0702-0.04510.17490.00960.314425.5612-0.6136.3375
51.2215-0.0097-1.0681.1281-0.04162.09050.0621-0.08170.13290.1469-0.0304-0.1001-0.18310.1849-0.03170.2545-0.0406-0.01520.02-0.01390.3087.108812.800217.4741
60.48590.13430.08190.26530.16441.19460.0773-0.08430.01620.07170.0104-0.1991-0.07060.342-0.08780.287-0.0516-0.0260.1254-0.00170.361618.9851.037921.0754
72.07390.5112-1.20491.2728-0.22773.15220.05280.19420.0129-0.0043-0.0539-0.4543-0.26621.3810.00110.4828-0.1465-0.02330.94840.08450.398321.936359.038360.4072
81.2997-0.30480.5821.25590.54183.64430.04510.1011-0.20270.0575-0.0516-0.10390.72710.69510.00650.51630.1051-0.01860.29460.01720.311411.06137.513576.05
91.10920.33850.01171.20020.36683.26550.07740.15820.06740.12470.0165-0.353-0.30221.1998-0.09390.3947-0.1402-0.04510.59310.08020.359118.075457.911874.0751
101.4503-0.33821.16270.61330.70243.5699-0.04430.32980.1415-0.23450.0701-0.1799-0.40160.7091-0.02580.6069-0.0089-0.03270.5180.03580.31725.294250.5631115.839
111.51990.0103-0.73661.20320.32943.9492-0.0413-0.04390.22490.153-0.0294-0.0962-0.69850.42570.07070.5709-0.143-0.03920.19620.00950.30995.909265.125297.8984
120.9896-0.18160.05410.51560.13152.05820.1172-0.04120.0619-0.0118-0.0676-0.1706-0.14980.8196-0.04960.5681-0.0519-0.0490.4950.05730.32818.963952.2021101.0896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 201
2X-RAY DIFFRACTION2A202 - 348
3X-RAY DIFFRACTION3A349 - 435
4X-RAY DIFFRACTION4B1 - 186
5X-RAY DIFFRACTION5B187 - 307
6X-RAY DIFFRACTION6B308 - 435
7X-RAY DIFFRACTION7C6 - 208
8X-RAY DIFFRACTION8C209 - 317
9X-RAY DIFFRACTION9C318 - 435
10X-RAY DIFFRACTION10D1 - 193
11X-RAY DIFFRACTION11D194 - 310
12X-RAY DIFFRACTION12D311 - 435

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