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- PDB-4dlf: Crystal structure of an amidohydrolase (COG3618) from burkholderi... -

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Basic information

Entry
Database: PDB / ID: 4dlf
TitleCrystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (TARGET EFI-500235) with bound ZN, space group P3221
ComponentsAmidohydrolase 2
KeywordsHYDROLASE / Amidohydrolase / enzyme function initiative / EFI / Cog3618 / Structural Genomics / TIM-barrel fold / Putative lactonase
Function / homology
Function and homology information


L-fucono-1,5-lactonase / fucose catabolic process / hydrolase activity / metal ion binding
Similarity search - Function
Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-fucono-1,5-lactonase / Putative amidohydrolase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.925 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Al Obaidi, N.F. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: to be published
Title: Crystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (target efi-500235) with bound ZN, space group P3221
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Al Obaidi, N.F. / Zencheck, W.D. / Imker, ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Al Obaidi, N.F. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 13, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_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: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,31410
Polymers33,9601
Non-polymers3549
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.300, 75.300, 142.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Amidohydrolase 2 / Putative amidohydrolase


Mass: 33960.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / Gene: Bmul_3602, BMULJ_04915 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9ANE4, UniProt: A0A0H3KNC4*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 7.5
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 0.5 mM ZnCl, 0.5 mM D-arabonate-1,4-lactone; Reservoir (20% Peg3350, 100 mM HEPES pH 7.5); Cryoprotection (Reservoir, 5 mM Zn, 25 mM ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 0.5 mM ZnCl, 0.5 mM D-arabonate-1,4-lactone; Reservoir (20% Peg3350, 100 mM HEPES pH 7.5); Cryoprotection (Reservoir, 5 mM Zn, 25 mM D-arabonate-1,4-lactone, 20% glycerol), sitting drop vapor diffuction, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.925→65.212 Å / Num. all: 36087 / Num. obs: 36087 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.138 / Net I/σ(I): 7.3
Reflection shell

Rmerge(I) obs: 0.021 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.92-2.035.70.42962051782.10699.9
2.03-2.1560.62953449371.30799.9
2.15-2.360.92778846490.82499.9
2.3-2.4961.52576343140.516100
2.49-2.725.92.32376440110.323100
2.72-3.045.93.92147136350.189100
3.04-3.515.87.41889332360.093100
3.51-4.35.78.51568227400.06899.8
4.3-6.095.58.21169221410.07299.3
6.09-38.3865.710.5706812460.05298.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DNM

4dnm


Resolution: 1.925→38.386 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8273 / SU ML: 0.21 / σ(F): 0 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1421 5.05 %random
Rwork0.1926 ---
all0.1944 28155 --
obs0.1944 28155 77.86 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.358 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 90.34 Å2 / Biso mean: 32.2636 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.2988 Å20 Å2-0 Å2
2---0.2988 Å2-0 Å2
3---0.5977 Å2
Refinement stepCycle: LAST / Resolution: 1.925→38.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 14 212 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122403
X-RAY DIFFRACTIONf_angle_d1.0823275
X-RAY DIFFRACTIONf_chiral_restr0.072341
X-RAY DIFFRACTIONf_plane_restr0.005432
X-RAY DIFFRACTIONf_dihedral_angle_d13.164856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9252-1.9940.351590.345135736610
1.994-2.07380.3321300.266586489425
2.0738-2.16820.2761730.27181651172448
2.1682-2.28250.27221670.24633172333993
2.2825-2.42540.25331870.230734013588100
2.4254-2.61270.24721860.214534013587100
2.6127-2.87550.28522020.204134043606100
2.8755-3.29140.22731850.191934333618100
3.2914-4.14610.20121950.163834633658100
4.1461-38.39320.19361870.16693588377598
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)
11.38710.6147-0.14421.98-0.39140.69660.0799-0.05840.13570.2822-0.04480.23-0.0717-0.0929-0.06970.2998-0.17170.04060.17240.00820.1278-35.647826.2266148.7378
22.29351.7832-1.53892.6733-1.49052.47520.1908-0.15030.08720.3308-0.1050.0553-0.1206-0.0226-0.09520.3708-0.1444-0.00050.16770.02280.0925-34.708220.0508158.3942
31.5564-0.019-1.60971.0366-0.13052.65590.1307-0.389-0.18630.3413-0.0965-0.23610.05170.2965-0.01450.5262-0.192-0.22690.31270.10550.2986-20.138412.7574160.218
43.41230.2014-0.88092.00760.67370.9901-0.022-0.0113-0.20.00650.1009-0.29070.00990.1661-0.01110.318-0.1922-0.09360.26780.03090.2-20.908613.6095148.3087
51.65490.907-0.49132.1958-0.44841.53520.0230.02-0.11930.10780.0354-0.34430.05050.0858-0.00230.2357-0.1392-0.07470.12660.00510.1979-20.95579.0354144.5275
61.2047-0.00230.58232.6388-0.94181.927-0.06910.1450.1513-0.1481-0.0205-0.26550.03110.06360.13970.1828-0.12860.01190.10460.00790.1247-27.135314.2014133.7691
70.94140.557-0.49772.621-1.22340.9371-0.12480.144-0.0574-0.27740.0627-0.21310.1771-0.02510.07670.2646-0.15770.01590.1634-0.00780.1734-28.01688.0585132.0006
84.7439-0.34950.30153.15831.44981.7840.05650.37330.4723-0.4553-0.026-0.1223-0.20790.0658-0.05310.2619-0.11630.01580.18980.07130.1453-32.066928.3994131.1823
90.35140.193-0.03030.5268-0.03890.14090.01350.032-0.0255-0.02570.0290.03650.0439-0.03190.03220.2403-0.189-0.03220.19060.03880.1541-37.000416.9905133.3431
100.3551-0.4543-0.18154.89735.30496.0539-0.030.1136-0.0138-0.1865-0.25190.81190.0417-0.42470.33790.2132-0.1499-0.06910.28380.0570.2495-45.366318.7588133.0858
111.3020.77920.06741.5559-0.07880.27450.0433-0.03550.0090.0338-0.00040.08960.0795-0.0903-0.02970.3202-0.2234-0.00390.25650.03050.2015-43.26737.635142.6699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:59)A3 - 59
2X-RAY DIFFRACTION2chain 'A' and (resseq 60:81)A60 - 81
3X-RAY DIFFRACTION3chain 'A' and (resseq 82:97)A82 - 97
4X-RAY DIFFRACTION4chain 'A' and (resseq 98:121)A98 - 121
5X-RAY DIFFRACTION5chain 'A' and (resseq 122:156)A122 - 156
6X-RAY DIFFRACTION6chain 'A' and (resseq 157:180)A157 - 180
7X-RAY DIFFRACTION7chain 'A' and (resseq 181:202)A181 - 202
8X-RAY DIFFRACTION8chain 'A' and (resseq 203:216)A203 - 216
9X-RAY DIFFRACTION9chain 'A' and (resseq 217:253)A217 - 253
10X-RAY DIFFRACTION10chain 'A' and (resseq 254:268)A254 - 268
11X-RAY DIFFRACTION11chain 'A' and (resseq 269:289)A269 - 289

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