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- PDB-4z48: Crystal structure of a DUF1329 family protein (DESPIG_00262) from... -

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Basic information

Entry
Database: PDB / ID: 4z48
TitleCrystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution
ComponentsUncharacterized protein
KeywordsStructural Biology / Unknown Function / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyPutative outer membrane lipoprotein-sorting protein / Outer membrane lipoprotein-sorting protein / Lipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / IODIDE ION / Outer membrane lipoprotein-sorting protein
Function and homology information
Biological speciesDesulfovibrio piger ATCC 29098 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation_author / entity_src_gen ...citation_author / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation_author.name / _entity_src_gen.pdbx_alt_source_flag ..._citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Feb 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.conn_type_id / _struct_conn.id / _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_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
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00913
Polymers57,7892
Non-polymers1,22111
Water9,998555
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3115
Polymers28,8941
Non-polymers4164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6998
Polymers28,8941
Non-polymers8047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.400, 56.340, 65.560
Angle α, β, γ (deg.)100.710, 97.040, 109.010
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 28894.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio piger ATCC 29098 (bacteria)
Gene: DESPIG_00262 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B6WQE2

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Non-polymers , 5 types, 566 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2000M Sodium Iodide, 20.0000% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97922 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.75→27.549 Å / Num. all: 53315 / Num. obs: 53315 / % possible obs: 95.6 % / Redundancy: 3.9 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.087 / Rsym value: 0.076 / Net I/av σ(I): 6.437 / Net I/σ(I): 8.8 / Num. measured all: 209473
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.75-1.840.5830.5041.51538038920.2930.5830.50412.294.2
1.8-1.8440.4840.4191.81523338550.2430.4840.4192.594.7
1.84-1.93.90.4290.3712.11442136540.2160.4290.3712.694.7
1.9-1.963.70.2660.2282.91334535800.1350.2660.228494
1.96-2.0240.2260.1953.81398135290.1130.2260.1954.795.1
2.02-2.0940.1760.1524.91348434010.0880.1760.1525.895.5
2.09-2.1740.1540.1335.51295032680.0770.1540.1336.795.4
2.17-2.263.80.1420.1224.91201831450.0720.1420.1228.695.2
2.26-2.363.90.1360.11861170730200.0690.1360.1187.494.9
2.36-2.4740.1160.10171136228730.0580.1160.1018.896
2.47-2.6140.1090.0947.31103427840.0550.1090.0949.996.3
2.61-2.7740.0950.0828.31045626360.0480.0950.08211.696.4
2.77-2.9640.0820.0719.4979924690.0410.0820.07113.196.9
2.96-3.240.0780.0689.8909422940.0390.0780.06815.196.9
3.2-3.540.0630.05411.9852721520.0310.0630.05417.997
3.5-3.9140.0590.05113765319350.0290.0590.05119.597.4
3.91-4.5240.0580.05113665716810.0290.0580.0512097.3
4.52-5.5340.0590.05112.2576814590.030.0590.05119.697.8
5.53-7.833.90.0870.0768.9435411060.0440.0870.07617.797.9
7.83-27.5493.90.080.0699.522505820.0410.080.06919.492.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER2.10.2refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→27.549 Å / Cor.coef. Fo:Fc: 0.9446 / Cor.coef. Fo:Fc free: 0.9254 / Occupancy max: 1 / Occupancy min: 0.3 / 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. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 4. IODINE (IOD), SODIUM (NA), CHLORIDE (CL) AND PEG FRAGMENTS MODELED ARE PRESENT IN PROTEIN OR CRYSTALLIZATION CONDITIONS. 5. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 2671 5.07 %RANDOM
Rwork0.2104 ---
obs0.2122 52699 94.55 %-
Displacement parametersBiso max: 99.99 Å2 / Biso mean: 32.5168 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.3375 Å2-0.4968 Å20.8796 Å2
2---0.3362 Å2-0.7848 Å2
3---1.6736 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 1.75→27.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 26 555 4519
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1945SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes589HARMONIC5
X-RAY DIFFRACTIONt_it4068HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion495SEMIHARMONIC5
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_contact4864SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4068HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5489HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion2.91
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2192 218 5.62 %
Rwork0.1806 3658 -
all0.1828 3876 -
obs--94.55 %
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)
10.6458-0.10390.45010.56520.03091.098-0.0422-0.07820.06680.03170.0317-0.0076-0.1066-0.00210.0105-0.11570.01740.00630.1983-0.0806-0.0978-18.172441.125975.4023
20.82860.05670.42040.7227-0.13071.48420.01270.0425-0.1154-0.0360.09160.0202-0.0111-0.1235-0.1042-0.13020.01240.00860.1891-0.0661-0.1098-4.712628.429842.3124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|29 - 268}A29 - 268
2X-RAY DIFFRACTION2{B|29 - 268}B29 - 268

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