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- PDB-4q7a: Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetyla... -

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Basic information

Entry
Database: PDB / ID: 4q7a
TitleCrystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus
ComponentsN-acetyl-ornithine/N-acetyl-lysine deacetylase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta fold / alpha-beta sandwich
Function / homology
Function and homology information


lysine biosynthetic process via aminoadipic acid / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / cobalt ion binding / zinc ion binding / cytoplasm
Similarity search - Function
[LysW]-lysine/[LysW]-ornithine hydrolase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Alpha-Beta Plaits - #360 / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...[LysW]-lysine/[LysW]-ornithine hydrolase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Alpha-Beta Plaits - #360 / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-ornithine/N-acetyl-lysine deacetylase
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.048 Å
AuthorsKim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus
Authors: Kim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: N-acetyl-ornithine/N-acetyl-lysine deacetylase
B: N-acetyl-ornithine/N-acetyl-lysine deacetylase
C: N-acetyl-ornithine/N-acetyl-lysine deacetylase
D: N-acetyl-ornithine/N-acetyl-lysine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,20413
Polymers156,4164
Non-polymers7889
Water19,2401068
1
A: N-acetyl-ornithine/N-acetyl-lysine deacetylase
B: N-acetyl-ornithine/N-acetyl-lysine deacetylase
C: N-acetyl-ornithine/N-acetyl-lysine deacetylase
D: N-acetyl-ornithine/N-acetyl-lysine deacetylase
hetero molecules

A: N-acetyl-ornithine/N-acetyl-lysine deacetylase
B: N-acetyl-ornithine/N-acetyl-lysine deacetylase
C: N-acetyl-ornithine/N-acetyl-lysine deacetylase
D: N-acetyl-ornithine/N-acetyl-lysine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,40826
Polymers312,8328
Non-polymers1,57618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area27640 Å2
ΔGint-204 kcal/mol
Surface area99110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.540, 119.540, 119.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
N-acetyl-ornithine/N-acetyl-lysine deacetylase


Mass: 39103.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / Gene: Sthe_0214 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: D1C6B5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1068 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M litium sulfate, 0.1 M phosphate-citrate pH 4.2, 20 %(w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.05→50 Å / Num. all: 105065 / Num. obs: 105065 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 21.67 Å2 / Rsym value: 0.052 / Net I/σ(I): 11.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5166 / Rsym value: 0.562 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.9_1678)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.048→48.78 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.61 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.171 5145 5.04 %random
Rwork0.154 ---
obs0.156 102060 96.96 %-
all-102060 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.3 Å2
Refinement stepCycle: LAST / Resolution: 2.048→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10391 0 45 1068 11504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310712
X-RAY DIFFRACTIONf_angle_d0.79214645
X-RAY DIFFRACTIONf_dihedral_angle_d12.6793845
X-RAY DIFFRACTIONf_chiral_restr0.0511680
X-RAY DIFFRACTIONf_plane_restr0.0051931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0479-2.08320.23031830.19813414359765
2.0832-2.12110.21722200.19544298451882
2.1211-2.16190.22852450.19524646489189
2.1619-2.2060.21342580.18974799505792
2.206-2.2540.21682530.18614924517793
2.254-2.30640.2112440.1814915515994
2.3064-2.36410.21052820.17724937521994
2.3641-2.4280.19362640.17484965522995
2.428-2.49950.19092740.1754953522794
2.4995-2.58010.19552580.17694981523995
2.5801-2.67230.20922700.17374985525595
2.6723-2.77930.19772630.17135010527395
2.7793-2.90580.2042640.16954963522795
2.9058-3.0590.18032560.16075002525895
3.059-3.25060.18972490.15395009525895
3.2506-3.50150.15732290.14635033526296
3.5015-3.85370.1462650.13325034529995
3.8537-4.41110.12142690.11264976524595
4.4111-5.55620.12662730.12235012528595
5.5562-48.72640.17452860.15645082536894
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)
10.85780.0180.3341.2055-0.49811.50270.1019-0.06160.0301-0.0274-0.07170.1348-0.059-0.2064-0.00190.1334-0.01970.01130.12230.0010.1035-28.181840.550826.4667
21.10590.407-0.24651.2765-0.25620.79080.1252-0.2109-0.10720.0693-0.12010.0641-0.05060.0786-0.02080.1378-0.00150.00970.12540.00040.123710.401750.225721.6686
31.06530.4765-0.08380.3154-0.15230.1520.176-0.1806-0.07430.0547-0.1005-0.11040.04480.1209-0.03750.192-0.06710.01390.1630.00880.1395-14.974537.904433.3036
41.01630.0816-0.55090.7623-0.0131.3721-0.036-0.0080.1396-0.0640.04360.0745-0.1804-0.08190.02280.1216-0.0167-0.00590.14430.00650.106119.302487.9931-41.2349
51.0720.1935-0.21511.1438-0.16220.9774-0.05290.106-0.0125-0.12530.0564-0.078-0.04890.0245-0.00440.1451-0.0039-0.0090.15330.01510.13679.561149.0494-36.3827
60.3850.5131-0.31250.574-0.33540.1284-0.15850.04710.0298-0.28470.1730.03090.1756-0.0825-0.0280.2214-0.08350.03240.21260.01490.179417.652469.61-49.6947
70.9328-0.2889-0.24081.08090.13911.2815-0.1781-0.0279-0.0968-0.11070.1353-0.0485-0.02150.0493-0.02070.1408-0.07320.0130.17870.01650.097126.620580.8322-45.8893
81.13-0.09320.49810.95890.03481.1138-0.0117-0.1811-0.12610.17630.06950.14970.033-0.3955-0.00640.17560.00910.0130.2280.03990.1599-11.051925.0351-2.3224
90.6671-0.1694-0.10430.65640.04991.18130.07440.0074-0.10340.0824-0.1099-0.05140.11520.0993-0.00610.17170.0357-0.01070.14310.03820.12632.594726.1613-4.2612
101.4397-0.0930.11372.8074-0.00511.2312-0.0240.08830.2966-0.1065-0.0993-0.0677-0.28660.168-0.00960.17730.0335-0.02060.18020.03930.157317.816556.2608-22.3031
110.4773-0.330.17970.89-0.45390.6162-0.0699-0.02360.00170.02260.0548-0.0497-0.02970.06270.02870.10430.04570.00410.18220.00750.123616.057940.0796-19.9688
120.90790.33370.12960.55930.02670.42590.17430.0305-0.28160.0114-0.1183-0.03250.31910.1238-0.03730.23180.0812-0.00810.19670.04730.22225.355516.6436-9.2966
130.9363-0.32860.3330.7527-0.35830.81150.16690.2614-0.467-0.0519-0.06520.00760.38410.0684-0.00910.2347-0.002-0.04390.09770.00080.2441-5.703316.4799-9.3027
140.89580.0263-0.27261.20020.48811.31480.01720.10330.0389-0.1486-0.0034-0.0811-0.17290.0270.00090.17540.02010.03040.17040.0240.14634.401566.8529-11.881
152.2162-0.67890.12730.7567-0.03120.8941-0.04720.0253-0.15710.0201-0.01050.04360.2715-0.08880.03860.2220.01630.02980.0791-0.00540.086315.244342.33218.5006
160.73890.161-0.51680.75510.01490.53820.17710.10570.0629-0.1221-0.1408-0.07520.09270.01960.01180.19140.04990.03970.13910.02980.130819.856347.01543.1876
170.71990.3067-0.17920.91550.00250.4638-0.00230.0076-0.06990.03420.0241-0.21820.08690.2183-0.02590.16280.0730.01180.22920.02430.16136.98750.7988-4.1482
180.889-0.3007-0.53520.93870.29891.0438-0.0653-0.08470.08430.08660.1055-0.36570.03250.25730.00040.1874-0.00420.02330.2232-0.01650.218941.308166.5401-2.6437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 163 )
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 257 )
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 361 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 163 )
5X-RAY DIFFRACTION5chain 'B' and (resid 164 through 257 )
6X-RAY DIFFRACTION6chain 'B' and (resid 258 through 313 )
7X-RAY DIFFRACTION7chain 'B' and (resid 314 through 361 )
8X-RAY DIFFRACTION8chain 'C' and (resid 10 through 123 )
9X-RAY DIFFRACTION9chain 'C' and (resid 124 through 165 )
10X-RAY DIFFRACTION10chain 'C' and (resid 166 through 185 )
11X-RAY DIFFRACTION11chain 'C' and (resid 186 through 265 )
12X-RAY DIFFRACTION12chain 'C' and (resid 266 through 313 )
13X-RAY DIFFRACTION13chain 'C' and (resid 314 through 361 )
14X-RAY DIFFRACTION14chain 'D' and (resid 9 through 165 )
15X-RAY DIFFRACTION15chain 'D' and (resid 166 through 209 )
16X-RAY DIFFRACTION16chain 'D' and (resid 210 through 249 )
17X-RAY DIFFRACTION17chain 'D' and (resid 250 through 313 )
18X-RAY DIFFRACTION18chain 'D' and (resid 314 through 353 )

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