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- PDB-2i9w: Crystal structure of a sec-c motif containing protein (psyc_2064)... -

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Basic information

Entry
Database: PDB / ID: 2i9w
TitleCrystal structure of a sec-c motif containing protein (psyc_2064) from psychrobacter arcticus at 1.75 A resolution
ComponentsHypothetical protein
KeywordsMETAL BINDING PROTEIN / Cystatin-like fold / sec-c motif fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / YchJ family protein, N-terminal zinc binding domain / : / YchJ, middle NTF2-like domain / SEC-C motif / SEC-C motif / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
SEC-C motif domain protein
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_265345.1) from Psychrobacter Arcticum 273-4 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1764
Polymers21,0091
Non-polymers1663
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.490, 54.690, 83.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein


Mass: 21009.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Gene: YP_265345.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4FPZ7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 0.2M MgCl2, 20.0% PEG-8000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94926,0.97939,0.97925
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.949261
20.979391
30.979251
ReflectionResolution: 1.75→29.501 Å / Num. obs: 19754 / % possible obs: 93.9 % / Biso Wilson estimate: 27.791 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.75-1.810.3612.25713301583.8
1.81-1.890.3032.76838360588
1.89-1.970.2293.55933313090.2
1.97-2.070.1724.46339334093.6
2.07-2.20.1216.26776359095.5
2.2-2.370.0977.66831361896.8
2.37-2.610.079.86949366497.1
2.61-2.990.05913.16896366297.6
2.990.04317.66813365098.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.501 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rwork: 0.194 / SU B: 4.648 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ZN200 IS COORDINATED TO THE SIDE CHAINS OF CYS 8, 10, 28 AND 29. ZN201 IS COORDINATED TO THE SIDE CHAINS OF CYS 167, 169, 178 AND ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ZN200 IS COORDINATED TO THE SIDE CHAINS OF CYS 8, 10, 28 AND 29. ZN201 IS COORDINATED TO THE SIDE CHAINS OF CYS 167, 169, 178 AND 179. ZN IS MODELED BASED ON ELECTRON DENSITY AND GEOMETRY, AND IS SUPPORTED BY X-RAY FLOURESCENCE EXPERIMENTS. (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) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (5) THE RESIDUES IN THE DISORDERED REGIONS OF A40-45 WERE NOT MODELLED. (6) THERE ARE UNMODELED DENSITIES NEAR A132 AND A56.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1007 5.1 %RANDOM
Rwork0.192 ---
obs0.19392 19707 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.135 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---0.26 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 3 127 1500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221429
X-RAY DIFFRACTIONr_bond_other_d0.0010.02940
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9431950
X-RAY DIFFRACTIONr_angle_other_deg0.90332307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6124.06859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37715230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.59155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined0.2350.2249
X-RAY DIFFRACTIONr_nbd_other0.1890.2905
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2680
X-RAY DIFFRACTIONr_nbtor_other0.0870.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.27
X-RAY DIFFRACTIONr_mcbond_it2.0963967
X-RAY DIFFRACTIONr_mcbond_other0.5053352
X-RAY DIFFRACTIONr_mcangle_it2.97851454
X-RAY DIFFRACTIONr_scbond_it4.7968593
X-RAY DIFFRACTIONr_scangle_it6.42311493
LS refinement shellResolution: 1.751→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 68 -
Rwork0.236 1350 -
obs-1418 98.88 %
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)
10.7903-0.332-0.21263.240.38763.03680.14720.0039-0.11170.1111-0.0837-0.20890.246-0.1805-0.0635-0.0468-0.0608-0.0285-0.02940.0255-0.019511.895911.024822.1427
21.1208-0.2910.56342.2314-0.38073.11290.08970.01640.0223-0.0065-0.0886-0.2232-0.09510.0708-0.0012-0.1175-0.0064-0.0072-0.06760.0207-0.028614.659523.612816.2532
32.32530.69894.48833.3019-0.202213.69960.05290.16-0.00980.05290.0097-0.1044-0.33710.3062-0.0626-0.15490.01550.0079-0.04130.0135-0.055111.532228.424617.252
41.5283-0.366-0.05531.6295-1.68714.8341-0.02930.06050.0431-0.0723-0.0305-0.0006-0.65920.00350.05980.07220.0175-0.0015-0.08210.0152-0.078910.574535.15683.586
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 392 - 40
2246 - 12347 - 124
33127 - 143128 - 144
44145 - 183146 - 184

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