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- PDB-3cnx: CRYSTAL STRUCTURE OF A PUTATIVE DEHYDRATASE FROM THE NTF2-LIKE FA... -

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Basic information

Entry
Database: PDB / ID: 3cnx
TitleCRYSTAL STRUCTURE OF A PUTATIVE DEHYDRATASE FROM THE NTF2-LIKE FAMILY (SAV_4671) FROM STREPTOMYCES AVERMITILIS AT 2.10 A RESOLUTION
ComponentsUncharacterized protein
KeywordsLYASE / PUTATIVE DEHYDRATASE / NTF2-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-PG6 / TRIETHYLENE GLYCOL / Unknown ligand / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (NP_825848.1) from Streptomyces avermitilis at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 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 / 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_asym_id / _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_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_asym_id / _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_asym_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_conn.ptnr2_label_seq_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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,37820
Polymers55,1063
Non-polymers1,27217
Water1,71195
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,75214
Polymers36,7372
Non-polymers1,01412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-19.9 kcal/mol
Surface area12510 Å2
MethodPISA
2
C: Uncharacterized protein
hetero molecules

C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,25312
Polymers36,7372
Non-polymers51610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area2990 Å2
ΔGint-21.2 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.000, 128.750, 44.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 7 - 156 / Label seq-ID: 8 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsSIZE-EXCLUSION CHROMATOGRAPHY CONFIRMS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Uncharacterized protein


Mass: 18368.623 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: DSM 46492 / JCM 5070 / NCIMB 12804 / NRRL 8165 / Gene: NP_825848.1, SAV4671 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q82EE4

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Non-polymers , 8 types, 112 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

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 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.04
Details: NANODROP, 34.5% PEG 400, 0.2M Magnesium chloride, 0.1M HEPES pH 7.04, 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: 0.91162, 0.97978
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979781
ReflectionResolution: 2.1→29.553 Å / Num. obs: 35037 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.671 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.170.4581.9101755897194.9
2.17-2.260.3732.5118576779197.8
2.26-2.360.2853.1111156391198
2.36-2.490.2243.9120296842197.7
2.49-2.640.1665.2111066308197.7
2.64-2.850.1077.9118746721198
2.85-3.130.06512.2113726401197.8
3.13-3.590.03222.5118236663198.1
3.59-4.510.01934.6114966480198
4.51-29.5530.01442.8116426445195.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.553 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.083 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.162
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 3. CHLORIDE, MAGNESIUM, PARTIAL PEG(S) AND GLYCEROL WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. 4. AN UNIDENTIFIED LIGAND (UNL) HAS BEEN TENTATIVELY MODELED AT WHAT APPEARS TO BE PUTATIVE ACTIVE SITE(S) WHICH COULD BE A PROTEASE-LIKE CATALYTIC TRIAD FORMED BY CYS59-HIS150-E109 OR A METAL BINDING SITE FORMED BY HIS61-HIS150-E109.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1752 5 %RANDOM
Rwork0.199 ---
obs0.201 34988 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.351 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--0.8 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 88 95 3404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223409
X-RAY DIFFRACTIONr_bond_other_d0.0010.022198
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.964655
X-RAY DIFFRACTIONr_angle_other_deg1.44735387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.923.876129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58715465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3081515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02662
X-RAY DIFFRACTIONr_mcbond_it0.7311.52162
X-RAY DIFFRACTIONr_mcbond_other0.191.5879
X-RAY DIFFRACTIONr_mcangle_it1.32123490
X-RAY DIFFRACTIONr_scbond_it2.09931247
X-RAY DIFFRACTIONr_scangle_it2.9054.51159
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A786MEDIUM POSITIONAL0.290.5
2B786MEDIUM POSITIONAL0.190.5
3C786MEDIUM POSITIONAL0.210.5
1A839LOOSE POSITIONAL0.415
2B839LOOSE POSITIONAL0.385
3C839LOOSE POSITIONAL0.385
1A786MEDIUM THERMAL0.682
2B786MEDIUM THERMAL0.542
3C786MEDIUM THERMAL0.592
1A839LOOSE THERMAL0.8210
2B839LOOSE THERMAL0.8710
3C839LOOSE THERMAL0.9210
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 116 -
Rwork0.247 2369 -
all-2485 -
obs--97.49 %
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)
13.01491.29-0.662.6928-0.75053.07030.0723-0.2359-0.29150.3037-0.2958-0.14620.15340.26140.2234-0.012-0.1317-0.0379-0.07580.0375-0.122386.21415.158534.6524
21.30170.8973-0.10492.5264-1.06742.2755-0.09450.1642-0.1187-0.1861-0.1703-0.26110.19550.32630.2648-0.085-0.0989-0.0110.00410.0344-0.097993.775524.621815.6337
31.84110.27980.53291.7911-0.66191.34750.17110.1037-0.1947-0.2359-0.065-0.06240.24220.0092-0.1061-0.06630.0161-0.037-0.1104-0.0209-0.0794105.248752.75292.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1578 - 158
2X-RAY DIFFRACTION2BB7 - 1578 - 158
3X-RAY DIFFRACTION3CC6 - 1567 - 157

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