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- PDB-4l8n: Crystal structure of a PDZ domain protein (BDI_1242) from Parabac... -

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Basic information

Entry
Database: PDB / ID: 4l8n
TitleCrystal structure of a PDZ domain protein (BDI_1242) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution
ComponentsPDZ domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / N-terminal and C-terminal PDZ domains / DUF4136 domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Double Stranded RNA Binding Domain - #670 / Domain of unknown function DUF4136 / Domain of unknown function (DUF4136) / PDZ domain / Pdz3 Domain / Double Stranded RNA Binding Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Double Stranded RNA Binding Domain - #670 / Domain of unknown function DUF4136 / Domain of unknown function (DUF4136) / PDZ domain / Pdz3 Domain / Double Stranded RNA Binding Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ETHANOL / PDZ domain protein
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a PDZ domain protein (BDI_1242) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PDZ domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9834
Polymers52,7941
Non-polymers1893
Water1,76598
1
A: PDZ domain protein
hetero molecules

A: PDZ domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9668
Polymers105,5892
Non-polymers3776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5330 Å2
ΔGint-50 kcal/mol
Surface area41770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.093, 104.093, 96.277
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-503-

MG

21A-683-

HOH

31A-696-

HOH

41A-697-

HOH

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Components

#1: Protein PDZ domain protein


Mass: 52794.312 Da / Num. of mol.: 1 / Fragment: UNP residues 21-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1242 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LBD9
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (21-476) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (21-476) 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 42.00% Ethanol, 0.0500M magnesium chloride, 0.1M TRIS pH 8.0, 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: 0.97882,0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978821
20.918371
ReflectionResolution: 2.5→48.138 Å / Num. obs: 21215 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.55 % / Biso Wilson estimate: 71.778 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.576.661.1471.5810286154499.5
2.57-2.640.912210187152599.9
2.64-2.710.6852.79574145099.7
2.71-2.80.5513.28822143299.7
2.8-2.890.3844.58992138399.1
2.89-2.990.2736.39250133899.9
2.99-3.10.2058.18907130999.8
3.1-3.230.15110.784491250100
3.23-3.370.1114.38142120399.9
3.37-3.540.0818.47553115499.7
3.54-3.730.06221.96368107398.1
3.73-3.950.05128.17196103999.8
3.95-4.230.04132.56614965100
4.23-4.560.03636628093699.9
4.56-50.03636.75481843100
5-5.590.04535.2433075097.5
5.59-6.460.04638.8469070299.9
6.46-7.910.04838.93682588100
7.91-11.180.03442.9245944997.4
11.18-48.140.0348.2166028297.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.138 Å / Cor.coef. Fo:Fc: 0.9503 / Cor.coef. Fo:Fc free: 0.9336 / Occupancy max: 1 / Occupancy min: 0.2 / 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. MG, MPD, AND EOH MODELED ARE PRESENT IN PROTEIN/CRYO CONDITIONS. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. OTHER REFINEMENT REMARKS: 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. MG, MPD, AND EOH MODELED ARE PRESENT IN PROTEIN/CRYO CONDITIONS. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 1077 5.09 %RANDOM
Rwork0.1863 ---
obs0.1879 21175 99.53 %-
Displacement parametersBiso max: 171.63 Å2 / Biso mean: 75.5429 Å2 / Biso min: 31.09 Å2
Baniso -1Baniso -2Baniso -3
1-5.1649 Å20 Å20 Å2
2--5.1649 Å20 Å2
3----10.3298 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 12 98 3685
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1694SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes524HARMONIC5
X-RAY DIFFRACTIONt_it3676HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
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_contact4078SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3676HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4987HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion3.09
LS refinement shellResolution: 2.5→2.62 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2685 141 5.04 %
Rwork0.2264 2656 -
all0.2286 2797 -
obs--99.53 %
Refinement TLS params.Method: refined / Origin x: -26.7405 Å / Origin y: 5.6661 Å / Origin z: 1.163 Å
111213212223313233
T-0.1889 Å20.0464 Å2-0.0159 Å2--0.0621 Å2-0.0993 Å2---0.0852 Å2
L0.573 °20.492 °20.4299 °2-1.8085 °21.4375 °2--1.9204 °2
S0.0489 Å °-0.0377 Å °-0.0802 Å °0.2318 Å °-0.1942 Å °0.1008 Å °0.1711 Å °-0.2253 Å °0.1453 Å °
Refinement TLS groupSelection details: {A|25 - 476}

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