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- PDB-3hk4: CRYSTAL STRUCTURE OF A PUTATIVE SNOAL-LIKE POLYKETIDE CYCLASE [CA... -

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Basic information

Entry
Database: PDB / ID: 3hk4
TitleCRYSTAL STRUCTURE OF A PUTATIVE SNOAL-LIKE POLYKETIDE CYCLASE [CARBOHYDRATE PHOSPHATASE] (MLR7391) FROM MESORHIZOBIUM LOTI AT 1.96 A RESOLUTION
ComponentsMlr7391 protein
KeywordsLYASE / NTF2-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologySnoaL-like domain 5 / SnoaL-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 / Mlr7391 protein
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (NP_107719.1) from Mesorhizobium loti at 1.96 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: 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: Mlr7391 protein
B: Mlr7391 protein
C: Mlr7391 protein
D: Mlr7391 protein


Theoretical massNumber of molelcules
Total (without water)62,8744
Polymers62,8744
Non-polymers00
Water5,098283
1
A: Mlr7391 protein
B: Mlr7391 protein


Theoretical massNumber of molelcules
Total (without water)31,4372
Polymers31,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-22 kcal/mol
Surface area12470 Å2
MethodPISA
2
C: Mlr7391 protein
D: Mlr7391 protein


Theoretical massNumber of molelcules
Total (without water)31,4372
Polymers31,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-18 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.183, 54.778, 63.844
Angle α, β, γ (deg.)88.770, 84.910, 73.560
Int Tables number1
Space group name H-MP1
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT A DIMER IS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Mlr7391 protein


Mass: 15718.579 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mlr7391, NP_107719.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q986E8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.24 Å3/Da / Density % sol: 45.13 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 0.3000 M magnesium chloride, 24.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.6, VAPOR DIFFUSION, SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97894,0.97833
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978941
30.978331
ReflectionResolution: 1.96→28.352 Å / Num. obs: 37927 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 2.02 % / Biso Wilson estimate: 26.47 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.82
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.96-2.030.2011.975466820186
2.03-2.110.1692.573736677186.3
2.11-2.210.1273.277497056187.2
2.21-2.320.0944.170236413187.2
2.32-2.470.0795.378787210188.2
2.47-2.660.0576.775236949188.9
2.66-2.930.0389.575977053189.8
2.93-3.350.02614.875177057191
3.35-4.210.0212276057219192
4.21-28.3520.01925.876477401194

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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
RefinementMethod to determine structure: MAD / Resolution: 1.96→28.352 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 8.089 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.152
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.UNKNOWN ELECTRON DENSITY IS OBSERVED NEAR TO GLU 35 IN THE CONSERVED ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1903 5 %RANDOM
Rwork0.177 ---
obs0.179 37925 96.7 %-
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 max: 82.13 Å2 / Biso mean: 35.285 Å2 / Biso min: 5.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.8 Å21.1 Å2
2---0.9 Å2-0.1 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.96→28.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 0 283 3934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224076
X-RAY DIFFRACTIONr_bond_other_d0.0020.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9375528
X-RAY DIFFRACTIONr_angle_other_deg0.94636604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7345530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.43625200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85115673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8411519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024781
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02842
X-RAY DIFFRACTIONr_nbd_refined0.2020.3685
X-RAY DIFFRACTIONr_nbd_other0.1770.32506
X-RAY DIFFRACTIONr_nbtor_refined0.1880.51825
X-RAY DIFFRACTIONr_nbtor_other0.090.52114
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.5435
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1380.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.399
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.522
X-RAY DIFFRACTIONr_mcbond_it2.46932750
X-RAY DIFFRACTIONr_mcbond_other0.57131062
X-RAY DIFFRACTIONr_mcangle_it3.23254080
X-RAY DIFFRACTIONr_scbond_it6.23481696
X-RAY DIFFRACTIONr_scangle_it8.225111448
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 141 -
Rwork0.227 2650 -
all-2791 -
obs--95.61 %
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)
10.39840.10.19891.4420.57911.214-0.0650.00170.02280.01240.0020.060.02890.02740.063-0.113-0.0054-0.0045-0.05950.0262-0.059740.510432.016927.3055
20.7876-0.6171-1.38351.54221.86254.0027-0.1190.1698-0.2428-0.0569-0.25940.31750.0436-0.3770.37840.0502-0.0079-0.00080.0965-0.02290.055139.726417.76933.1786
30.5938-0.4559-0.14452.80950.90080.7892-0.0498-0.0314-0.0001-0.11210.0964-0.1132-0.09320.1772-0.0465-0.101-0.0207-0.0077-0.04290.0186-0.024630.6863.604330.2943
41.0104-0.397-0.38050.79770.35612.1147-0.0014-0.0395-0.0193-0.0101-0.02130.0156-0.3869-0.00150.0227-0.0423-0.0035-0.0139-0.0740.0138-0.063516.322.302945.7924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 117
2X-RAY DIFFRACTION2B0 - 117
3X-RAY DIFFRACTION3C1 - 117
4X-RAY DIFFRACTION4D1 - 117

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