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- PDB-3cgh: Crystal structure of a susd homolog (bt_3984) from bacteroides th... -

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Basic information

Entry
Database: PDB / ID: 3cgh
TitleCrystal structure of a susd homolog (bt_3984) from bacteroides thetaiotaomicron vpi-5482 at 1.70 A resolution
ComponentsSusD homolog
KeywordsMETAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


SusD-like / Susd and RagB outer membrane lipoprotein / 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
Similarity search - Domain/homology
ACETATE ION / SusD homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules.
Authors: Bakolitsa, C. / Xu, Q. / Rife, C.L. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / ...Authors: Bakolitsa, C. / Xu, Q. / Rife, C.L. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Lam, W.W. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMar 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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.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_conn_type.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: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6913
Polymers57,5661
Non-polymers1242
Water12,683704
1
A: SusD homolog
hetero molecules

A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3816
Polymers115,1322
Non-polymers2494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area1950 Å2
ΔGint-11.3 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.780, 125.270, 174.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

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Components

#1: Protein SusD homolog


Mass: 57566.195 Da / Num. of mol.: 1 / Fragment: Residues 23-537
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Species: Bacteroides thetaiotaomicron / Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50 / Gene: NP_812895.1, BT_3984 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A0N7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CONSTRUCT CONTAINS RESIDUES 23-537 OF 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: NANODROP, 0.2M NH4OAc, 30.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97911, 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 21, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979111
30.979221
ReflectionResolution: 1.7→28.039 Å / Num. obs: 60062 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.794 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.3282.52118711140197.1
1.76-1.830.2583.12203111511199.4
1.83-1.910.20542146211189199.3
1.91-2.020.1485.42398012489199.3
2.02-2.140.1067.32104310937199.4
2.14-2.310.0819.42287511880199.4
2.31-2.540.06511.62198211339199.1
2.54-2.90.047152205311297198.5
2.9-3.660.03220.82264711457197.8
3.66-28.0390.02527.42246511225196

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.039 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.99 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083
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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ACT IS MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. ZN IS MODELED BASED ON AN X-RAY FLOURESCENCE SCAN, ANOMALOUS DIFFERENCE FOURIERS, AND COORDINATION GEOMETRY. 6. RESIDUE GLY 41 IS A RAMACHANDRAN OUTLIER, AND IS PRESENT IN POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.166 3037 5.1 %RANDOM
Rwork0.14 ---
obs0.142 60025 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.202 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 5 704 4652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224156
X-RAY DIFFRACTIONr_bond_other_d0.0010.022719
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9335694
X-RAY DIFFRACTIONr_angle_other_deg1.41336655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21225.268205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91715642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9251517
X-RAY DIFFRACTIONr_chiral_restr0.10.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214806
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02843
X-RAY DIFFRACTIONr_mcbond_it0.7741.52590
X-RAY DIFFRACTIONr_mcbond_other0.2681.51048
X-RAY DIFFRACTIONr_mcangle_it1.28924183
X-RAY DIFFRACTIONr_scbond_it2.23731566
X-RAY DIFFRACTIONr_scangle_it3.5974.51496
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 228 -
Rwork0.189 4096 -
all-4324 -
obs--97.61 %
Refinement TLS params.Method: refined / Origin x: -19.915 Å / Origin y: -52.104 Å / Origin z: 20.37 Å
111213212223313233
T-0.0333 Å20.0351 Å2-0.0053 Å2--0.0276 Å2-0.0065 Å2---0.0482 Å2
L0.5402 °2-0.1535 °2-0.0047 °2-0.4763 °20.1319 °2--0.4645 °2
S0.0633 Å °0.0265 Å °0.0087 Å °-0.0958 Å °-0.0495 Å °-0.0043 Å °-0.0414 Å °-0.0069 Å °-0.0138 Å °

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