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- PDB-3u1w: Crystal structure of a Calcium binding protein (BDI_1975) from Pa... -

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Basic information

Entry
Database: PDB / ID: 3u1w
TitleCrystal structure of a Calcium binding protein (BDI_1975) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
ComponentsHypothetical PERIPLASMIC PROTEIN
KeywordsMETAL BINDING PROTEIN / BLIP-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #360 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative beta-lactamase-inhibitor-like PepSY-like domain-containing protein
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical PERIPLASMIC PROTEIN (BDI_1975) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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_asym_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
Revision 1.5Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical PERIPLASMIC PROTEIN
B: Hypothetical PERIPLASMIC PROTEIN
C: Hypothetical PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,48229
Polymers87,2643
Non-polymers1,21826
Water14,880826
1
A: Hypothetical PERIPLASMIC PROTEIN
B: Hypothetical PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,80616
Polymers58,1762
Non-polymers63014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-85 kcal/mol
Surface area25610 Å2
MethodPISA
2
C: Hypothetical PERIPLASMIC PROTEIN
hetero molecules

C: Hypothetical PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,35326
Polymers58,1762
Non-polymers1,17724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5930 Å2
ΔGint-96 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.258, 152.840, 165.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 29 - 277 / Label seq-ID: 5 - 253

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT A DIMER IS A SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Hypothetical PERIPLASMIC PROTEIN


Mass: 29088.045 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_1975 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LDE6

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Non-polymers , 5 types, 852 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 26-334) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 26-334) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-277 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: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 20.0% 2-propanol, 0.2M calcium chloride, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97938
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2011
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: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2→29.99 Å / Num. all: 101909 / Num. obs: 101909 / % possible obs: 100 % / Redundancy: 6.3 % / Rsym value: 0.141 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.056.30.9950.74699374760.995100
2.05-2.116.30.8590.94570672640.859100
2.11-2.176.30.6821.14484071190.682100
2.17-2.246.30.5831.34345768870.583100
2.24-2.316.30.5251.24212566720.525100
2.31-2.396.30.4351.74081464610.435100
2.39-2.486.30.36823953262470.368100
2.48-2.586.30.3182.43809260170.318100
2.58-2.76.30.25533651257830.255100
2.7-2.836.30.2023.73506055390.202100
2.83-2.986.30.1664.43329352590.166100
2.98-3.166.30.1375.13142549730.137100
3.16-3.386.30.1116.12974447020.111100
3.38-3.656.30.0877.62772943900.087100
3.65-46.30.0798.32554440460.079100
4-4.476.30.0699.12299336500.069100
4.47-5.166.30.0699.32037532530.069100
5.16-6.326.20.0857.91732527860.085100
6.32-8.946.10.0897.51322921750.08999.9
8.94-29.995.80.078.8701512100.0797

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.6.0116refinement
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.917 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117
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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. CALCIUM (CA), CHLORIDE (CL), AND ACETATE (ACT) FROM THE CRYSTALLIZATION AND 1,2-ETHANEDIOL USED AS A CRYOPROTECTANT WERE MOLDELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 5088 5 %RANDOM
Rwork0.1893 ---
obs0.1906 101900 99.93 %-
Displacement parametersBiso max: 79.48 Å2 / Biso mean: 34.4015 Å2 / Biso min: 9.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20 Å2
2---0.65 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5983 0 59 826 6868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226271
X-RAY DIFFRACTIONr_bond_other_d0.0010.024008
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9378559
X-RAY DIFFRACTIONr_angle_other_deg0.79539883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4055787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49926.564326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.13151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.902155
X-RAY DIFFRACTIONr_chiral_restr0.0550.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021215
X-RAY DIFFRACTIONr_bond_it1.4592.4536271
X-RAY DIFFRACTIONr_bond_other0.2722.4694006
X-RAY DIFFRACTIONr_angle_it2.3753.6438538
X-RAY DIFFRACTIONr_angle_others1.3453.7129883
X-RAY DIFFRACTIONr_torsion_it4.3197.4952139
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3178 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.50.5
BMEDIUM POSITIONAL0.310.5
CMEDIUM POSITIONAL0.440.5
AMEDIUM THERMAL3.792
BMEDIUM THERMAL3.182
CMEDIUM THERMAL3.292
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 322 -
Rwork0.278 6834 -
all-7156 -
obs--99.94 %
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)
10.44410.2865-0.05340.50630.25311.41950.0236-0.1002-0.01190.0543-0.05120.02210.0930.10970.02760.07060.0263-0.02990.0450.00420.060324.706720.009539.4891
20.5242-0.1563-0.23270.57950.22821.6643-0.03940.0186-0.01340.0179-0.0208-0.03430.04230.19530.06020.0717-0.0023-0.03670.03610.02890.074531.1711-15.563219.023
30.75290.35750.52590.17670.2420.6417-0.0543-0.08150.144-0.0215-0.04720.0647-0.0857-0.05950.10140.09350.0122-0.04680.0258-0.02180.05185.43940.38619.644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 277
2X-RAY DIFFRACTION2B29 - 277
3X-RAY DIFFRACTION3C28 - 277

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