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- PDB-3p1u: Crystal structure of a SusD homolog (BDI_0600) from Parabacteroid... -

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Basic information

Entry
Database: PDB / ID: 3p1u
TitleCrystal structure of a SusD homolog (BDI_0600) from Parabacteroides distasonis ATCC 8503 AT 2.05 A resolution
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / SusD/RagB family nutrient-binding outer membrane lipoprotein
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a SusD homolog (YP_001301998.1) from Parabacteroides distasonis ATCC 8503 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 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 ...database_2 / 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
Revision 1.4Oct 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
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: SusD homolog
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5753
Polymers119,4792
Non-polymers961
Water10,665592
1
A: SusD homolog


Theoretical massNumber of molelcules
Total (without water)59,7391
Polymers59,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8352
Polymers59,7391
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.242, 130.242, 114.822
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein SusD homolog


Mass: 59739.395 Da / Num. of mol.: 2 / Fragment: sequence database residues 26-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: DSM 20701 / NCTC 11152 / Gene: BDI_0600 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L9L2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 26-553) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 26-553) 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / pH: 4.47
Details: 1.13M ammonium sulfate, 0.1M phosphate-citrate pH 4.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97916,0.97860
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979161
30.97861
ReflectionResolution: 2.05→28.701 Å / Num. obs: 69272 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.65 Å2 / Rmerge(I) obs: 0.252 / Rsym value: 0.252 / Net I/σ(I): 7.3
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 0.8 / Rsym value: 0.965 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.2.5data processing
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.05→28.7 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.84 / 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. SULFATE FROM THE CRYSTALLIZATION BUFFER IS MODELED INTO THE STRUCTURE. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. LYS 64 ON THE A AND B SUBUNITS AND PRO 462 ON THE A AND B SUBUNITS ARE RAMACHANDRAN OUTLIERS, BUT THEIR MODELING IS SUPPORTED BY ELECTRON DENSITY. 5. THE R AND R-FREE VALUES ARE ELEVATED COMPARED WITH OTHER STRUCTURES IN THE PDB REFINED AT THE SAME RESOLUTION, AND THIS CAN LIKELY BE ATTRIBUTED TO UNIDENTIFIED CRYSTAL DISORDERS THAT RESULT IN REDUCED DATA QUALITY. 6. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3503 5.06 %RANDOM
Rwork0.243 ---
obs0.244 69269 --
Displacement parametersBiso mean: 18.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.6302 Å20 Å20 Å2
2--1.6302 Å20 Å2
3----3.2604 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8073 0 5 592 8670
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018338HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.3711343HARMONIC10
X-RAY DIFFRACTIONt_dihedral_angle_d2866SINUSOIDAL10
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes233HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1216HARMONIC5
X-RAY DIFFRACTIONt_it8338HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion13.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1085SEMIHARMONIC5
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_contact10979SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2216 249 4.9 %
Rwork0.2017 4834 -
all0.2027 5083 -
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)
10.25270.0579-0.02130.3714-0.02520.2603-0.00180.0112-0.00260.0008-0.00270.0222-0.0026-0.04580.0045-0.08680.00210.0087-0.05850.0234-0.0542-42.447313.01475.1758
20.3152-0.09610.08680.4956-0.07730.2410.02230.002-0.00930.05040.01190.0521-0.0243-0.0104-0.0342-0.0933-0.0040.0047-0.08090.0247-0.0385-43.6159-8.6921127.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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