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- PDB-3b7c: CRYSTAL STRUCTURE OF A NTF-2 LIKE PROTEIN OF UNKNOWN FUNCTION (SO... -

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Basic information

Entry
Database: PDB / ID: 3b7c
TitleCRYSTAL STRUCTURE OF A NTF-2 LIKE PROTEIN OF UNKNOWN FUNCTION (SO_0125) FROM SHEWANELLA ONEIDENSIS MR-1 AT 1.70 A RESOLUTION
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / NTF-2 LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


asparaginase / asparaginase activity
Similarity search - Function
Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Periplasmic L-asparaginase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF-2 like protein of unknown function (NP_715767.1) from Shewanella oneidensis at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8868
Polymers14,4781
Non-polymers4087
Water2,918162
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,77316
Polymers28,9572
Non-polymers81614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area2160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.190, 66.190, 126.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein


Mass: 14478.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: NP_715767.1, SO_0125 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8EKG8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. REMARK 999

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 0.2M CaCl2, 20.0% Isopropanol, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9797, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97971
30.97951
ReflectionResolution: 1.7→29.298 Å / Num. obs: 18701 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.49 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.59
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.5612.8163723249197.1
1.76-1.830.4363.91913533971100
1.83-1.910.3215.21863532941100
1.91-2.020.2038.12098837021100
2.02-2.140.136121838232371100
2.14-2.310.115.9197853481199.9
2.31-2.540.07719.71930233931100
2.54-2.90.0528.91882133321100
2.9-3.660.03144.3191933457199.8
3.66-29.2980.02454.7184133369198.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.298 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.906 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1
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. CHLORIDE ION FROM THE CRYSTALLIZATION CONDITIONS AND ETHYLENE GLYCOL FROM THE CRYO CONDITIONS ARE MODELED IN THE STRUCTURE. 5. THE UNEXPLAINED ELECTRON DENSITY AROUND RESIDUE 44 WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 953 5.1 %RANDOM
Rwork0.184 ---
obs0.186 18638 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 25 162 1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221143
X-RAY DIFFRACTIONr_bond_other_d0.0010.02785
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.961550
X-RAY DIFFRACTIONr_angle_other_deg0.88431917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50225.18554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1415208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.549156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021305
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02228
X-RAY DIFFRACTIONr_nbd_refined0.2180.2219
X-RAY DIFFRACTIONr_nbd_other0.20.2850
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2523
X-RAY DIFFRACTIONr_nbtor_other0.0880.2638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2124
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.220
X-RAY DIFFRACTIONr_mcbond_it2.383742
X-RAY DIFFRACTIONr_mcbond_other0.6153274
X-RAY DIFFRACTIONr_mcangle_it2.7951110
X-RAY DIFFRACTIONr_scbond_it5.7858528
X-RAY DIFFRACTIONr_scangle_it7.6211440
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 73 -
Rwork0.232 1265 -
all-1338 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: -8.4327 Å / Origin y: 28.8831 Å / Origin z: 1.3111 Å
111213212223313233
T-0.0453 Å20.0017 Å2-0.0062 Å2-0.0273 Å20.0251 Å2---0.0258 Å2
L1.1943 °20.9562 °2-0.535 °2-1.5679 °2-0.4634 °2--0.9847 °2
S-0.0716 Å °-0.2068 Å °-0.108 Å °-0.025 Å °-0.0627 Å °-0.0761 Å °0.0154 Å °0.0701 Å °0.1342 Å °

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