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- PDB-3n58: Crystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from bru... -

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Basic information

Entry
Database: PDB / ID: 3n58
TitleCrystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / Adenosylhomocysteinase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.39 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form
Authors: SSGCID / Gardberg, A. / Sankaran, B. / Abendroth, J. / Staker, B.
History
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 21, 2012Group: Refinement description
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 6, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)205,55814
Polymers201,9864
Non-polymers3,57310
Water12,827712
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.450, 165.230, 184.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.941421, 0.144589, 0.304665), (-0.166555, -0.9849, -0.047241), (0.293234, -0.095217, 0.951287)-45.9706, -8.88521, 5.73854
2given(-0.753924, 0.654966, 0.051172), (0.655705, 0.745382, 0.120236), (0.040608, 0.124203, -0.991426)-27.369, 5.68512, 65.0356
3given(0.687536, -0.590714, -0.422316), (-0.587839, -0.794207, 0.153887), (-0.426309, 0.14245, -0.893291)3.74981, -27.6716, 54.2434
4given(-0.940897, 0.146729, 0.305259), (-0.168164, -0.984731, -0.044999), (0.293996, -0.093673, 0.951205)-46.0521, -8.91219, 5.69407
5given(-0.754787, 0.653934, 0.051632), (0.654726, 0.746175, 0.120653), (0.040373, 0.124872, -0.991351)-27.4357, 5.69578, 65.0528
6given(0.68785, -0.591053, -0.421329), (-0.588058, -0.794048, 0.153867), (-0.4255, 0.141928, -0.89376)3.70821, -27.6632, 54.2808
7given(-0.915809, -0.079193, 0.393728), (-0.043334, -0.955157, -0.292911), (0.399268, -0.285313, 0.87131)-45.8599, -5.08914, 9.16551
8given(-0.753953, 0.655596, 0.041826), (0.654783, 0.744824, 0.128436), (0.05305, 0.124222, -0.990835)-26.9655, 5.44875, 65.315
9given(0.675962, -0.592196, -0.438612), (-0.594728, -0.789838, 0.149849), (-0.435172, 0.159562, -0.886095)4.34113, -27.5193, 53.676
10given(-0.914748, -0.084482, 0.395092), (-0.03987, -0.954245, -0.296355), (0.402052, -0.286842, 0.869526)-45.7995, -4.88123, 9.31441
11given(-0.753102, 0.656572, 0.041839), (0.655794, 0.744078, 0.127598), (0.052646, 0.123533, -0.990943)-26.907, 5.47159, 65.2888
12given(0.677513, -0.591933, -0.436568), (-0.5941, -0.790351, 0.149633), (-0.433615, 0.157987, -0.887141)4.27247, -27.5183, 53.7129
13given(-0.758053, 0.650384, 0.048543), (0.65062, 0.748958, 0.125521), (0.04528, 0.126735, -0.990903)-27.4402, 5.47779, 65.1982
14given(0.689091, -0.589297, -0.421762), (-0.586058, -0.795505, 0.153975), (-0.42625, 0.141074, -0.893537)3.73472, -27.6187, 54.2532
15given(-0.757702, 0.650702, 0.049745), (0.651113, 0.74863, 0.124918), (0.044044, 0.12704, -0.990919)-27.4878, 5.49983, 65.1791
16given(0.688494, -0.589905, -0.421887), (-0.586717, -0.794992, 0.154115), (-0.42631, 0.141421, -0.893454)3.73551, -27.6454, 54.2379

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Components

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


Mass: 50496.410 Da / Num. of mol.: 4 / Fragment: UNP residues 8-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: ahcY, BAB1_2099 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YQX8, adenosylhomocysteinase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: JCSG SCREEN CONDITION D12: 20% V/ V GLYCEROL, 16% W/V PEG 8000, 40 MM POTASSIUM PHOSPHATE, PROTEIN AT 80 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 30, 2010
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
20.97741
ReflectionResolution: 2.39→49.27 Å / Num. all: 83567 / Num. obs: 83542 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 34.18 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 16.09
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 7 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.6 / Num. unique all: 6114 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(PHENIX.REFINE: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
RefinementStarting model: PDB entry 2ZIZ

2ziz


Resolution: 2.39→49.27 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3987 4.98 %RANDOM
Rwork0.172 ---
all0.175 83567 --
obs0.175 83542 --
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.51 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 32.99 Å2
Baniso -1Baniso -2Baniso -3
1-14.175 Å2-0 Å2-0 Å2
2---6.972 Å20 Å2
3----7.566 Å2
Refinement stepCycle: LAST / Resolution: 2.39→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13850 0 236 712 14798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.192
X-RAY DIFFRACTIONf_bond_d0.008
LS refinement shellResolution: 2.39→2.42 Å
RfactorNum. reflection% reflection
Rfree0.3294 117 -
Rwork0.2205 --
obs-2638 100 %
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)
10.07140.03610.01950.01450.02090.014-0.0174-0.09560.06070.0651-0.00290.0998-0.0397-0.09180.0152-0.1793-0.0007-0.03560.1707-0.0390.1652-33.44-29.1845.0453
20.00330.01110.00030.04260.02530.0294-0.00080.0450.01860.0110.0644-0.0525-0.0450.0378-0.0423-0.01050.01640.01360.1418-0.03050.1135-10.5045-24.984520.1376
30.0563-0.06110.06520.0528-0.03890.0806-0.0353-0.0439-0.0423-0.0028-0.00330.0424-0.0869-0.07430.038-0.07730.1304-0.06850.0184-0.00050.1146-35.5095-7.1139.8863
40.0145-0.0170.040.0338-0.08240.2362-0.0041-0.0297-0.01020.08220.00950.0285-0.4462-0.0465-0.01740.3508-0.0682-0.00110.12380.03130.0525-8.411721.74823.796
50.06380.0169-0.02050.0315-0.08810.28970.00430.0149-0.01970.11150.00260.1048-0.3306-0.0257-0.01260.26520.06320.00480.031-0.00740.101-27.106412.868829.3763
60.03310.0243-0.01290.0853-0.03790.0523-0.02040.0040.0065-0.08440.0316-0.0138-0.00060.0404-0.02050.0774-0.08180.03820.0838-0.03930.0301-8.2675-0.5554.9519
70.18340.08450.07520.2820.12070.08250.1090.00020.01840.353-0.07470.03150.20740.0035-0.03390.3378-0.02530.02440.0716-0.01090.0699-20.5057-37.601754.8217
80.09770.0376-0.03270.0540.00980.0272-0.01510.06790.07640.047-0.00910.07950.0023-0.05190.0130.0930.00350.07810.1043-0.02130.122-34.7181-17.476541.5379
90.16690.08220.09160.18980.09120.0673-0.03890.0946-0.00350.08880.038-0.0356-0.01410.09610.00530.0736-0.0243-0.09550.0826-0.01280.0959-4.5317-21.73652.8282
100.1645-0.0388-0.08440.04560.03190.14390.081-0.0338-0.0550.1015-0.0678-0.076-0.38230.12-0.00820.4899-0.1709-0.03720.0971-0.0040.0412-4.00316.290259.4253
110.35470.00910.04560.00240.01080.2067-0.0006-0.0308-0.1081-0.00610.046-0.0699-0.13450.1228-0.04160.1035-0.1494-0.04660.1002-0.06010.0812.88471.390436.6415
120.17090.00010.03550.1565-0.0070.0847-0.0673-0.05350.02050.1618-0.0069-0.0095-0.10560.01190.06340.2948-0.03830.0650.0816-0.04650.0492-20.070.70759.3957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 6:229
2X-RAY DIFFRACTION2chain A and resseq 230:379
3X-RAY DIFFRACTION3chain A and resseq 380:466
4X-RAY DIFFRACTION4chain B and resseq 6:229
5X-RAY DIFFRACTION5chain B and resseq 230:379
6X-RAY DIFFRACTION6chain B and resseq 380:466
7X-RAY DIFFRACTION7chain C and resseq 6:229
8X-RAY DIFFRACTION8chain C and resseq 230:379
9X-RAY DIFFRACTION9chain C and resseq 380:466
10X-RAY DIFFRACTION10chain D and resseq 6:229
11X-RAY DIFFRACTION11chain D and resseq 230:379
12X-RAY DIFFRACTION12chain D and resseq 380:466

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