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- PDB-2ia7: Crystal structure of putative tail lysozyme (NP_952040.1) from GE... -

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Basic information

Entry
Database: PDB / ID: 2ia7
TitleCrystal structure of putative tail lysozyme (NP_952040.1) from GEOBACTER SULFURREDUCENS at 1.44 A resolution
ComponentsTail lysozyme, putative
KeywordsUNKNOWN FUNCTION / NP_952040.1 / putative tail lysozyme / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyIraD/Gp25-like / Baseplate wedge protein gp25 / Nuclear Transport Factor 2; Chain: A, - #40 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / NITRATE ION / Phage baseplate outer wedge protein (Acidic lysozyme), putative
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.44 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative tail lysozyme (NP_952040.1) from GEOBACTER SULFURREDUCENS at 1.44 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 7, 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 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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). SEEREMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE 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 FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail lysozyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1573
Polymers15,0331
Non-polymers1242
Water2,162120
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)40.270, 43.332, 64.636
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 Tail lysozyme, putative


Mass: 15032.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: NP_952040.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74EH6
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.97 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.1
Details: 0.2M LiNO3, 20.0% PEG 3350, pH 7.1, 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: 0.94926,0.97925,0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.949261
20.979251
30.979391
ReflectionResolution: 1.44→43.315 Å / Num. obs: 19105 / % possible obs: 90.4 % / Redundancy: 3.92 % / Biso Wilson estimate: 23.067 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.44-1.491.920.4391.8188298248.9
1.49-1.552.120.3752.33145148270.6
1.55-1.622.420.30734370180487.7
1.62-1.713.250.2454.66843210697
1.71-1.813.540.186.76954196399.8
1.81-1.953.570.10510.675792124100
1.95-2.153.580.06615.57646213599.7
2.15-2.463.550.04820.275522127100
2.46-3.13.510.04324.67580215899.5
3.1-43.32.350.03528.77444222397.8

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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
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.44→43.315 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.74 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.073
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 0.7 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL FACTORS ONLY. 4. THE N-TERMINAL 0-22 IS DISODERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 978 5.1 %RANDOM
Rwork0.168 ---
obs0.169 19064 90.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.112 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.8 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.44→43.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 8 120 998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022919
X-RAY DIFFRACTIONr_bond_other_d0.0020.02629
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9851254
X-RAY DIFFRACTIONr_angle_other_deg0.95631535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21822.56439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94315163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4741510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
X-RAY DIFFRACTIONr_nbd_refined0.2020.2151
X-RAY DIFFRACTIONr_nbd_other0.2070.2685
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2445
X-RAY DIFFRACTIONr_nbtor_other0.0860.2535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.219
X-RAY DIFFRACTIONr_mcbond_it2.2463615
X-RAY DIFFRACTIONr_mcbond_other0.4393229
X-RAY DIFFRACTIONr_mcangle_it2.825936
X-RAY DIFFRACTIONr_scbond_it4.1448367
X-RAY DIFFRACTIONr_scangle_it5.61311312
LS refinement shellResolution: 1.44→1.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 42 -
Rwork0.291 725 -
obs-767 50.73 %
Refinement TLS params.Method: refined / Origin x: 25.9332 Å / Origin y: 11.9793 Å / Origin z: 41.2949 Å
111213212223313233
T-0.0343 Å2-0.0042 Å20.0061 Å2--0.0055 Å2-0.004 Å2---0.0089 Å2
L0.6448 °20.17 °2-0.0818 °2-0.9084 °2-0.4153 °2--1.1968 °2
S-0.017 Å °0.0106 Å °0.048 Å °0.0287 Å °-0.0011 Å °-0.0156 Å °-0.0778 Å °0.0419 Å °0.0181 Å °
Refinement TLS groupSelection: ALL

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