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- PDB-3pf0: Crystal structure of an Imelysin-like protein (Psyc_1802) from PS... -

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Basic information

Entry
Database: PDB / ID: 3pf0
TitleCrystal structure of an Imelysin-like protein (Psyc_1802) from PSYCHROBACTER ARCTICUM 273-4 at 2.15 A resolution
ComponentsImelysin-like protein
KeywordsUNKNOWN FUNCTION / PUTATIVE METALLOENDOPEPTIDASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


M75 peptidase, HXXE motif / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / A middle domain of Talin 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Imelysin-like domain-containing protein
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an Imelysin-like protein (Psyc_1802) from PSYCHROBACTER ARCTICUM 273-4 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Oct 9, 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: Imelysin-like protein


Theoretical massNumber of molelcules
Total (without water)38,9041
Polymers38,9041
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.674, 69.131, 165.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

DetailsCRYSTAL PACKING SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Imelysin-like protein


Mass: 38904.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Strain: 273-4 / Gene: Psyc_1802 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q4FQQ8
#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
Sequence detailsTHE CONSTRUCT (RESIDUES 27-389) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 27-389) 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, 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: 0.9795,0.9537,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.95371
30.97931
ReflectionResolution: 2.15→45.602 Å / Num. obs: 19285 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.316 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.99
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.230.619269751976199.9
2.23-2.320.4422.867431891199.9
2.32-2.420.3293.764391802199.8
2.42-2.550.2594.669821949199.8
2.55-2.710.1826.467591894199.9
2.71-2.920.1189.568381909199.9
2.92-3.210.07713.867631900199.8
3.21-3.670.04920.667631938199.9
3.67-4.610.03526.366181932199.4
4.61-45.6020.0328.568972062198.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→45.602 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9279 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. THE FOLLOWING REGION HAS POOR DENSITY: A319-327. REGION A28-65 IS DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 986 5.11 %RANDOM
Rwork0.1823 ---
obs0.184 19284 --
Displacement parametersBiso max: 126.13 Å2 / Biso mean: 47.343 Å2 / Biso min: 14.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.0684 Å20 Å20 Å2
2--7.389 Å20 Å2
3----6.3206 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 0 217 2574
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1154SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes360HARMONIC5
X-RAY DIFFRACTIONt_it2440HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion348SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3038SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2440HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3341HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion2.66
LS refinement shellResolution: 2.15→2.27 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2454 149 5.37 %
Rwork0.2053 2625 -
all0.2073 2774 -
Refinement TLS params.Method: refined / Origin x: 11.3256 Å / Origin y: 18.0514 Å / Origin z: -28.1989 Å
111213212223313233
T-0.1326 Å2-0.0914 Å20.0363 Å2--0.1279 Å2-0.0326 Å2---0.0064 Å2
L1.2661 °2-0.1088 °20.0334 °2-1.5142 °2-0.0778 °2--1.2068 °2
S0.204 Å °-0.2598 Å °0.0337 Å °0.1597 Å °-0.0868 Å °-0.023 Å °-0.028 Å °0.0483 Å °-0.1173 Å °
Refinement TLS groupSelection details: { A|* }

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