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- PDB-1ztp: X-ray structure of gene product from homo sapiens Hs.433573 -

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Basic information

Entry
Database: PDB / ID: 1ztp
TitleX-ray structure of gene product from homo sapiens Hs.433573
ComponentsBasophilic leukemia expressed protein BLES03
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hs.433573 / P5326 / BLES03 / BC010512 / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / Center for Eukaryotic Structural Genomics
Function / homologyBasophilic leukemia-expressed protein Bles03-like / Basophilic leukemia-expressed protein Bles03 / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Translation Initiation factor eIF- 4e-like / RNA binding / 2-Layer Sandwich / Alpha Beta / UPF0696 protein C11orf68
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The structure at 2.5 A resolution of human basophilic leukemia-expressed protein BLES03.
Authors: Bitto, E. / Bingman, C.A. / Robinson, H. / Allard, S.T. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE THREE COPIES OF THE APPARENT MONOMERIC FORM OF THE BIOLOGICAL MOLECULE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basophilic leukemia expressed protein BLES03
B: Basophilic leukemia expressed protein BLES03
C: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)82,8013
Polymers82,8013
Non-polymers00
Water3,909217
1
A: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)27,6001
Polymers27,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)27,6001
Polymers27,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)27,6001
Polymers27,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
4
A: Basophilic leukemia expressed protein BLES03

C: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)55,2012
Polymers55,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area5950 Å2
ΔGint-19 kcal/mol
Surface area31980 Å2
MethodPISA
5
A: Basophilic leukemia expressed protein BLES03
B: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)55,2012
Polymers55,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-13 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.547, 116.809, 123.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
12A
22C

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111MSEMSEGLYGLYAA30 - 8330 - 83
211MSEMSEGLYGLYBB30 - 8330 - 83
311MSEMSEGLYGLYCC30 - 8330 - 83
421ASPASPLEULEUAA92 - 25092 - 250
521ASPASPLEULEUBB92 - 25092 - 250
621ASPASPLEULEUCC92 - 25092 - 250
112GLNGLNGLYGLYAA84 - 9184 - 91
212GLNGLNGLYGLYCC84 - 9184 - 91

NCS ensembles :
ID
1
2

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Components

#1: Protein Basophilic leukemia expressed protein BLES03


Mass: 27600.342 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hs.433573 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9H3H3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10 MG/ML PROTEIN, 1.2 M SODIUM CITRATE, 0.100 M TRIS, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC / Detector: CCD / Date: May 5, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (111) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 12.3 % / Av σ(I) over netI: 13.35 / Number: 31664 / Rmerge(I) obs: 0.106 / Χ2: 1.05 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 31664 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.165010010.0480.962
4.896.1610010.0640.947
4.274.8910010.0681.041
3.884.2710010.0750.982
3.613.8810010.0851.053
3.393.6199.910.1011.165
3.223.3999.710.1271.178
3.083.2299.610.1621.166
2.963.089910.211.127
2.862.9699.110.2681.073
2.772.8698.710.3391.04
2.692.7797.710.3951.054
2.622.6995.910.4690.998
2.562.6295.210.5080.982
2.52.5693.110.5970.94
ReflectionResolution: 2.5→50 Å / Num. obs: 31664 / % possible obs: 98.6 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 13.353
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 9 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.675 / % possible all: 93.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3.69 Å / D res low: 43.98 Å / FOM : 0.299 / FOM acentric: 0.327 / FOM centric: 0 / Reflection: 18562
Phasing MAD setR cullis: 0.735 / R cullis acentric: 0.703 / R cullis centric: 10 / R kraut: 0.02 / R kraut acentric: 0.02 / R kraut centric: 0.022 / Highest resolution: 3.69 Å / Lowest resolution: 43.98 Å / FOM : 0.299 / FOM acentric: 0.328 / FOM centric: 0 / Loc: 20.483 / Loc acentric: 20.507 / Loc centric: 20.466 / Power: 1.399 kW / Power acentric: 1.378 / Power centric: 1.602
Phasing MAD set shell

ID: 1 / R cullis centric: 10 / FOM centric: 0

Resolution (Å)R cullisR cullis acentricR krautR kraut acentricR kraut centricFOM FOM acentricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
7.37-43.980.560.510.0240.0230.0290.3870.46621.01221.05621.2482.1842.1882.165
5.85-7.370.6020.570.0270.0270.0350.3980.44418.0318.04118.1211.9741.9582.103
5.12-5.850.6890.6590.0220.0220.0250.3490.38218.69618.70818.8061.5971.5971.594
4.65-5.120.7660.7370.0170.0180.0160.3130.33819.87719.88219.9291.3221.321.35
4.32-4.650.8120.7810.0160.0160.0120.2690.29121.00521.01321.0891.1331.1361.094
4.06-4.320.8490.820.0170.0170.0140.2410.25821.06521.0721.1270.960.9571
3.86-4.060.8920.8640.0190.0190.0140.2230.23821.99222.00122.0950.8250.8230.851
3.69-3.860.9020.8770.020.0210.0140.2050.21822.37222.37222.3720.7360.7360.742
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
7.37-43.980.38810.466602348
5.85-7.370.39730.442302330
5.12-5.850.34860.381202349
4.65-5.120.31230.337502336
4.32-4.650.26860.2902332
4.06-4.320.23940.256102347
3.86-4.060.22280.237702334
3.69-3.860.20630.218202186
Phasing dmFOM : 0.59 / FOM acentric: 0.59 / FOM centric: 0.59 / Reflection: 31594 / Reflection acentric: 28112 / Reflection centric: 3482
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-43.9670.930.930.815081083425
4.5-7.10.860.880.7443623664698
3.6-4.50.840.850.7653904747643
3.1-3.60.70.710.653724835537
2.7-3.10.440.440.3894158629786
2.5-2.70.220.220.2255475154393

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.401data extraction
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.124 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1607 5.103 %RANDOM
Rwork0.188 ---
obs0.19118 31489 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.987 Å20 Å2
3----0.637 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 0 217 5513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9487420
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54522.727242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30215823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841547
X-RAY DIFFRACTIONr_chiral_restr0.0980.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024229
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22245
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23673
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.75123460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.33855432
X-RAY DIFFRACTIONr_scbond_it5.90382303
X-RAY DIFFRACTIONr_scangle_it7.9101988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1615loose positional0.815
12B1615loose positional0.95
13C1615loose positional0.65
21A56loose positional0.575
22C56loose positional0.575
14A1615loose thermal7.7310
15B1615loose thermal5.3110
16C1615loose thermal5.3710
21A56loose thermal3.5710
22C56loose thermal3.5710
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 118 -
Rwork0.275 1902 -
obs--86.96 %

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