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- PDB-4ecg: Crystal structure of a putative iron-regulated protein A precurso... -

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Basic information

Entry
Database: PDB / ID: 4ecg
TitleCrystal structure of a putative iron-regulated protein A precursor (BDI_2603) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
ComponentsPutative iron-regulated protein A
KeywordsHYDROLASE / Imelysin-like protein / putative metalloendopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Iron-regulated protein A, imelysin-like domain / M75 peptidase, HXXE motif / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative iron-regulated protein A
Similarity search - Component
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative iron-regulated protein A precursor (BDI_2603) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: Putative iron-regulated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,51112
Polymers41,8771
Non-polymers63411
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.892, 113.892, 75.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-655-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative iron-regulated protein A


Mass: 41876.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: ATCC 8503 / Gene: BDI_2603 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LF58
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-403 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40.00% polyethylene glycol 400, 0.200M calcium acetate, 0.1M HEPES pH 7.5, NANODROP, 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: 0.91837,0.97949
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2012 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
ReflectionResolution: 2.3→29.124 Å / Num. obs: 21402 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.286 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.380.4861.88379393696.4
2.38-2.480.3442.59596445299.3
2.48-2.590.2713.38742403899.3
2.59-2.730.1854.79134422399
2.73-2.90.1326.48996414899.2
2.9-3.120.0849.88916410599.1
3.12-3.430.05314.58930412498.1
3.43-3.930.03421.28951412397.1
3.93-4.930.02726.88690402596.8
4.930.02229.38876410496.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.124 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.16 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.172
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. CALCIUM (CA) AND PEG400 (1PE) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 1097 5.1 %RANDOM
Rwork0.1617 ---
obs0.1632 21391 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 129.42 Å2 / Biso mean: 55.4796 Å2 / Biso min: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2---1.4 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 26 114 2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022886
X-RAY DIFFRACTIONr_bond_other_d0.0020.021883
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9593916
X-RAY DIFFRACTIONr_angle_other_deg1.03734637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31826.288132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49115473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.948157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 87 -
Rwork0.265 1430 -
all-1517 -
obs--98.76 %
Refinement TLS params.Method: refined / Origin x: 96.652 Å / Origin y: 3.71 Å / Origin z: 5.993 Å
111213212223313233
T0.0467 Å20.0021 Å2-0.0685 Å2-0.0491 Å20.0452 Å2--0.1603 Å2
L1.626 °20.309 °2-0.006 °2-1.8716 °20.4868 °2--0.5646 °2
S0.1774 Å °-0.0891 Å °-0.2982 Å °0.0537 Å °-0.0663 Å °-0.0822 Å °-0.0104 Å °-0.0928 Å °-0.1111 Å °

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