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- PDB-3db7: Crystal structure of a putative calcium-regulated periplasmic pro... -

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Entry
Database: PDB / ID: 3db7
TitleCrystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution
Componentsputative calcium-regulated periplasmic protein
KeywordsCa-BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyInhibitor of vertebrate lysozyme, Ivy - #30 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Putative periplasmic protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of putative calcium-regulated periplasmic protein of unknown function (NP_809836.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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 / 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_alt_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: putative calcium-regulated periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0356
Polymers14,7901
Non-polymers2445
Water3,495194
1
A: putative calcium-regulated periplasmic protein
hetero molecules

A: putative calcium-regulated periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,07012
Polymers29,5812
Non-polymers48910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3320 Å2
ΔGint-77 kcal/mol
Surface area12730 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.170, 48.420, 44.610
Angle α, β, γ (deg.)90.00, 113.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3-

CA

21A-334-

HOH

DetailsAUTHORS STATE THAT ONLY WHEN CA1 AND CA2 ARE INCLUDED IN THE CALCULATION, DOES PISA (v1.14) PREDICT THAT A STABLE DIMER COULD BE A PROBABLE QUATERNARY STRUCTURE. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING (SEC+SLS) WITHOUT ADDED CALCIUM SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. WHEN A SAMPLE WAS RUN WITH 0.2 M CALCIUM CHLORIDE IN THE MOBILE PHASE (SIMILAR CONCENTRATION TO THAT IN THE CRYSTALLIZATION REAGENT), THE SEC+SLS RESULTS SHOWED PRIMARILY DIMER.

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Components

#1: Protein putative calcium-regulated periplasmic protein


Mass: 14790.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: NP_809836.1, BT_0923 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A994
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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 CLONED CONSTRUCT CONTAINS RESIDUES 20-145 OF THE FULL LENGTH PROTEIN.

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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: 44.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7., NANODROP, pH 7.3, 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: 0.91837,0.97947,0.97891
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 4, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979471
30.978911
ReflectionResolution: 1.4→24.922 Å / Num. obs: 23150 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 2.149 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.44
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID
1.4-1.450.5361.51
1.45-1.510.36921
1.51-1.580.2812.71
1.58-1.660.2113.61
1.66-1.760.1554.81
1.76-1.90.0937.41
1.9-2.090.04612.41
2.09-2.390.036161
2.39-3.010.02720.81
3.01-24.920.01732.11

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→24.922 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.134 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.071
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ETHYLENE GLYCOL AND CALCIUM IONS FROM THE CRYSTALLIZATION COND ARE MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.19824 1172 5.1 %RANDOM
Rwork0.16034 ---
obs0.16228 23150 90.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.15 Å2
2--0.24 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.4→24.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 11 194 1218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221131
X-RAY DIFFRACTIONr_bond_other_d0.0010.02771
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9651539
X-RAY DIFFRACTIONr_angle_other_deg1.09631902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12226.73152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48215209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.545151
X-RAY DIFFRACTIONr_chiral_restr0.1020.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211293
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02207
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6263697
X-RAY DIFFRACTIONr_mcbond_other0.513271
X-RAY DIFFRACTIONr_mcangle_it2.61551150
X-RAY DIFFRACTIONr_scbond_it3.9318434
X-RAY DIFFRACTIONr_scangle_it5.98411389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 76 -
Rwork0.258 1644 -
obs--91.98 %
Refinement TLS params.Method: refined / Origin x: 5.4168 Å / Origin y: 48.0223 Å / Origin z: 9.8704 Å
111213212223313233
T-0.0143 Å2-0.0043 Å2-0.0026 Å2--0.0308 Å20.0052 Å2---0.025 Å2
L1.2557 °20.012 °20.1457 °2-0.3124 °20.0582 °2--0.4953 °2
S0.0117 Å °-0.0362 Å °-0.0013 Å °0.0069 Å °-0.0177 Å °-0.0076 Å °0.0011 Å °0.0328 Å °0.006 Å °

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