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- PDB-3f8x: Crystal structure of a putative delta-5-3-ketosteroid isomerase (... -

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Basic information

Entry
Database: PDB / ID: 3f8x
TitleCrystal structure of a putative delta-5-3-ketosteroid isomerase (eca2236) from pectobacterium atrosepticum scri1043 at 1.55 A resolution
Componentsputative delta-5-3-ketosteroid isomerase
KeywordsISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative delta-5-3-ketosteroid isomerase (YP_050331.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: putative delta-5-3-ketosteroid isomerase
B: putative delta-5-3-ketosteroid isomerase
C: putative delta-5-3-ketosteroid isomerase
D: putative delta-5-3-ketosteroid isomerase


Theoretical massNumber of molelcules
Total (without water)66,2034
Polymers66,2034
Non-polymers00
Water14,214789
1
A: putative delta-5-3-ketosteroid isomerase
B: putative delta-5-3-ketosteroid isomerase


Theoretical massNumber of molelcules
Total (without water)33,1022
Polymers33,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-19 kcal/mol
Surface area11740 Å2
MethodPISA
2
C: putative delta-5-3-ketosteroid isomerase
D: putative delta-5-3-ketosteroid isomerase


Theoretical massNumber of molelcules
Total (without water)33,1022
Polymers33,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-19 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.780, 51.600, 66.310
Angle α, β, γ (deg.)79.41, 79.74, 61.89
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT STATIC LIGHT SCATTERING MEASUREMENTS INDICATE THAT THE DIMER IS A BIOLOGICAL SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
putative delta-5-3-ketosteroid isomerase


Mass: 16550.861 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Gene: ECA2236, YP_050331.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6D504
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.64 %
Description: THE DATA PROCESSING STATISTICS REPORTED HERE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20.0000% PEG-6000, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97934,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2008 / 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
20.979341
30.979221
ReflectionResolution: 1.55→28.964 Å / Num. obs: 80729 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 9.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.610.4271.4190.4
1.61-1.670.3281.8193.3
1.67-1.750.2322.5193.8
1.75-1.840.1583.5194.3
1.84-1.950.1085.2194.4
1.95-2.10.0688195.2
2.1-2.310.04611.3195.2
2.31-2.650.03414.4196.2
2.65-3.330.02320.7196.5
3.33-28.9640.01728.2196.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementResolution: 1.55→25.31 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.477 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.THIS TARGET SHOWS STRUCTURAL SIMILARITY TO KETO-STEROID ISOMERASES BELONGING TO THE NTF2-LIKE FOLD. THE PUTATIVE ACTIVE SITE IS LOCATED IN THE VICINITY OF TYR 59 NEAR SEVERAL UN-EXPLANINED DIFFERENCE ELECTRON DENSITIES THAT WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 4016 5 %RANDOM
Rwork0.15822 ---
obs0.15971 76705 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.32 Å20.14 Å2
2--1.39 Å20.29 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 0 789 4833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224431
X-RAY DIFFRACTIONr_bond_other_d0.0010.022844
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9526094
X-RAY DIFFRACTIONr_angle_other_deg0.92336993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2085591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17624.925201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60315690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1791521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025207
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
X-RAY DIFFRACTIONr_nbd_refined0.2280.3984
X-RAY DIFFRACTIONr_nbd_other0.1910.33135
X-RAY DIFFRACTIONr_nbtor_refined0.1830.52312
X-RAY DIFFRACTIONr_nbtor_other0.0910.52244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5957
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.551
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.76933025
X-RAY DIFFRACTIONr_mcbond_other0.45831125
X-RAY DIFFRACTIONr_mcangle_it2.4454618
X-RAY DIFFRACTIONr_scbond_it4.05681745
X-RAY DIFFRACTIONr_scangle_it5.418111476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 291 -
Rwork0.261 5455 -
obs--91.95 %
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)
11.17650.0391-0.50390.29260.15781.4003-0.0185-0.02930.0394-0.00140.0183-0.0320.01560.18510.0002-0.01680.0048-0.0201-0.017-0.0045-0.003395.037858.969493.6262
21.213-0.0067-0.44860.3255-0.14121.2781-0.057-0.0231-0.08360.01140.0124-0.01750.09390.01460.0446-0.00140.0026-0.0047-0.0533-0.0036-0.01275.126749.6729101.8656
30.8442-0.2603-0.30080.35940.1061.0915-0.0193-0.0142-0.0639-0.0146-0.02020.03160.10160.04660.0395-0.0106-0.0087-0.0018-0.0387-0.0013-0.011595.899444.77459.2541
40.8762-0.0473-0.59560.50970.11671.7870.01590.11630.01770.00320.01310.04340.0038-0.3574-0.029-0.0418-0.0118-0.01150.0250.0064-0.022775.71255.463165.1157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 146
2X-RAY DIFFRACTION2B17 - 147
3X-RAY DIFFRACTION3C16 - 147
4X-RAY DIFFRACTION4D16 - 147

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