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- PDB-3ff2: Crystal structure of an uncharacterized cystatin fold protein (sa... -

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Basic information

Entry
Database: PDB / ID: 3ff2
TitleCrystal structure of an uncharacterized cystatin fold protein (saro_2299) from novosphingobium aromaticivorans dsm at 1.90 A resolution
Componentsuncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily
KeywordsUNKNOWN FUNCTION / Ntf2 superfamily / 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 / ACETATE ION / SnoaL-like domain-containing protein
Function and homology information
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily (YP_497570.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.percent_possible_all / _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 / 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 27, 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: uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1472
Polymers13,0881
Non-polymers591
Water3,405189
1
A: uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily
hetero molecules

A: uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2944
Polymers26,1762
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2040 Å2
ΔGint-6 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.860, 47.860, 160.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily


Mass: 13087.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Gene: Saro_2299, YP_497570.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G5Y7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97870,0.97814
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 12, 2008 / 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
20.97871
30.978141
ReflectionResolution: 1.9→28.571 Å / Num. obs: 15445 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.049 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 5.652
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.956.30.5851.3699911150.585100
1.95-26.20.5231.4681210960.523100
2-2.066.20.4151.8662410600.415100
2.06-2.126.20.3871.9635410170.387100
2.12-2.196.20.2872.5629410140.287100
2.19-2.276.20.2612.860589770.26199.9
2.27-2.366.20.2293.157409200.22999.9
2.36-2.456.20.1923.656229080.19299.8
2.45-2.566.20.1564.453978760.15699.8
2.56-2.696.10.1185.751478390.11899.7
2.69-2.836.20.1076.149608060.10799.3
2.83-36.10.0917.146117510.09199.6
3-3.216.10.0817.643807220.08199.4
3.21-3.476.10.0738.340106550.07398.7
3.47-3.86.10.0610.337656180.0698.5
3.8-4.2560.05610.433725590.05698.1
4.25-4.9160.0629.930355100.06298.2
4.91-6.015.80.0619.625644410.06197.9
6.01-8.55.60.0512.319253450.0595.8
8.5-28.5814.90.03716.810552160.03793.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.571 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.52 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.125
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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. 4. AN ACETATE (ACT) ION FROM CRYSTALLIZATION CONDITION IS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 768 5 %RANDOM
Rwork0.187 ---
obs0.189 15374 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.89 Å2 / Biso mean: 33.86 Å2 / Biso min: 20.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 4 189 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022970
X-RAY DIFFRACTIONr_bond_other_d0.0010.02640
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9441321
X-RAY DIFFRACTIONr_angle_other_deg1.30631549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8175125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.19523.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53515153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.875159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02210
X-RAY DIFFRACTIONr_mcbond_it1.8623613
X-RAY DIFFRACTIONr_mcbond_other0.5663248
X-RAY DIFFRACTIONr_mcangle_it2.7695986
X-RAY DIFFRACTIONr_scbond_it5.0758357
X-RAY DIFFRACTIONr_scangle_it6.93911335
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 57 -
Rwork0.273 1052 -
all-1109 -
obs--99.82 %
Refinement TLS params.Method: refined / Origin x: 1.3105 Å / Origin y: 6.6322 Å / Origin z: 27.5892 Å
111213212223313233
T-0.0848 Å20.0154 Å20.0333 Å2--0.0368 Å20.0159 Å2---0.0655 Å2
L1.3339 °2-0.1776 °20.1902 °2-1.4692 °2-0.4164 °2--2.1422 °2
S0.0573 Å °0.0469 Å °0.0367 Å °-0.0045 Å °-0.0581 Å °0.0292 Å °0.0103 Å °-0.0119 Å °0.0008 Å °

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