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- PDB-3lho: Crystal structure of putative hydrolase (YP_751971.1) from Shewan... -

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Basic information

Entry
Database: PDB / ID: 3lho
TitleCrystal structure of putative hydrolase (YP_751971.1) from Shewanella frigidimarina NCIMB 400 at 1.80 A resolution
ComponentsPutative hydrolase
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


2-oxoadipate dioxygenase/decarboxylase / dioxygenase activity
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 - #50 / Domain of unknown function DUF1338 / 2-oxoadipate dioxygenase/decarboxylase / DUF1338 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / 2-oxoadipate dioxygenase/decarboxylase
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative hydrolase (YP_751971.1) from Shewanella frigidimarina NCIMB 400 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,08812
Polymers29,9661
Non-polymers1,12211
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.098, 75.035, 91.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative hydrolase


Mass: 29965.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Strain: NCIMB 400 / Gene: Sfri_3296 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q07XY2

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Non-polymers , 6 types, 215 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.57
Details: 1.3000M ammonium sulfate, 2.2500% polyethylene glycol 400, 15.0000% Glycerol, 0.1M HEPES pH 7.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97949,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
30.979341
ReflectionResolution: 1.8→28.961 Å / Num. obs: 27317 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.535 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.860.6951.39109468196.6
1.86-1.940.4931.910710547598.7
1.94-2.030.3452.710254521199
2.03-2.130.2583.49378478198.8
2.13-2.270.1754.710594536698.9
2.27-2.440.1369748495098.9
2.44-2.690.0977.810338521998.9
2.69-3.070.06610.99918499998.9
3.07-3.870.03917.410266513598.2
3.870.03223.510195501996.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→45.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.789 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE METAL PRESENT IN THE PUTATIVE ACTIVE SITE WAS TENTATIVELY ASSIGNED AS NICKLE (NI) BASED ON X-RAY FLURORESCENCE SPECTROSCOPY AND ANOMALOUS DIFFERENCE FOURIERS. NICKLE IONS WERE PRESENT DURING PURIFICATION AS CHELATING AGENT. 5. GLYCEROL (GOL), SULFATE (SO4) AND POLYETHYLENE GLYCOL FRAGMENTS (PEG AND PG4) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1366 5 %RANDOM
Rwork0.173 ---
obs0.175 27263 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.81 Å2 / Biso mean: 23.911 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å20 Å2
2---1.87 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 67 204 2265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222134
X-RAY DIFFRACTIONr_bond_other_d0.0010.021415
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9592893
X-RAY DIFFRACTIONr_angle_other_deg0.91433468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27324.94999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79415337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.972156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_mcbond_it1.87531282
X-RAY DIFFRACTIONr_mcbond_other0.5973518
X-RAY DIFFRACTIONr_mcangle_it2.78152071
X-RAY DIFFRACTIONr_scbond_it5.0228852
X-RAY DIFFRACTIONr_scangle_it6.89411816
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 90 -
Rwork0.296 1849 -
all-1939 -
obs--97.1 %
Refinement TLS params.Method: refined / Origin x: 19.9667 Å / Origin y: 13.7145 Å / Origin z: 28.7525 Å
111213212223313233
T0.0154 Å2-0.0072 Å2-0.0092 Å2-0.0149 Å2-0.0018 Å2--0.0268 Å2
L0.2433 °2-0.2532 °20.1738 °2-0.9846 °2-0.5047 °2--1.148 °2
S0.0351 Å °-0.0033 Å °-0.0171 Å °-0.1061 Å °0.0106 Å °0.074 Å °0.0903 Å °-0.0186 Å °-0.0457 Å °

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