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- PDB-4exr: Crystal structure of a putative lipoprotein (CD1622) from Clostri... -

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Basic information

Entry
Database: PDB / ID: 4exr
TitleCrystal structure of a putative lipoprotein (CD1622) from Clostridium difficile 630 at 1.85 A resolution
ComponentsPutative lipoprotein
KeywordsUNKNOWN FUNCTION / YPEB domain dimer / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNuclear Transport Factor 2; Chain: A, - #40 / PepSY domain / Peptidase propeptide and YPEB domain / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / PHOSPHATE ION / Peptidase propeptide and ypeb domain protein
Function and homology information
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative lipoprotein (CD1622) from Clostridium difficile 630 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 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.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
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4843
Polymers20,3661
Non-polymers1182
Water1,874104
1
A: Putative lipoprotein
hetero molecules

A: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9686
Polymers40,7322
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area1470 Å2
ΔGint-38 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.631, 77.631, 84.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Putative lipoprotein


Mass: 20366.051 Da / Num. of mol.: 1 / Fragment: UNP residues 33-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_16220 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q186H8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 33-205) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 33-205) 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.20M sodium chloride, 40.00% polyethylene glycol 400, 0.1M Na/K phosphate pH 6.2, 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: 0.97903,0.91837,0.97845
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.918371
30.978451
ReflectionResolution: 1.85→28.639 Å / Num. all: 22697 / Num. obs: 22697 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rsym value: 0.093 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.95.30.8170.9864316260.817100
1.9-1.955.60.591.2902416240.5999.9
1.95-2.016.30.4591.6965615410.459100
2.01-2.076.20.3791.9943715310.379100
2.07-2.145.90.3362.2874114750.33699.9
2.14-2.215.80.2682.8832214360.26899.8
2.21-2.295.20.2283.1723713810.22899.6
2.29-2.395.80.2043.6763613250.20499.9
2.39-2.496.20.1664.4802212900.166100
2.49-2.626.10.1355.2755812300.13599.8
2.62-2.7660.125.6709411730.12100
2.76-2.935.70.0986.6628011080.09899.8
2.93-3.135.60.0867.3581510410.08699.5
3.13-3.386.30.0817.863009970.08199.9
3.38-3.76.10.0718.954909040.07199.5
3.7-4.145.70.06210.647598290.062100
4.14-4.785.20.05610.738347320.05698.2
4.78-5.8560.05910.938566390.059100
5.85-8.275.20.0611.126465110.0699
8.27-28.6395.30.05212.216183040.05295.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
PHENIX1.7.3refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.639 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.78 / Stereochemistry target values: MLHL
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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4.A SODIUM ION AND PHOSPHATE MOLECULE FROM THE PURIFICATION/CRYSTALLIZATION SOLUTIONS HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflection
Rfree0.21 1151 5.09 %
Rwork0.1844 --
obs0.1856 22606 99.35 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.591 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 108.6 Å2 / Biso mean: 41.9168 Å2 / Biso min: 19.06 Å2
Baniso -1Baniso -2Baniso -3
1-6.6748 Å20 Å2-0 Å2
2--6.6748 Å2-0 Å2
3----13.3495 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 6 104 1334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081304
X-RAY DIFFRACTIONf_angle_d1.0641767
X-RAY DIFFRACTIONf_chiral_restr0.077197
X-RAY DIFFRACTIONf_plane_restr0.004231
X-RAY DIFFRACTIONf_dihedral_angle_d13.07515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.93420.3141430.29392591273499
1.9342-2.03620.23561490.22442622277199
2.0362-2.16370.21031320.202426642796100
2.1637-2.33070.2221580.1912620277899
2.3307-2.56510.20191620.188226542816100
2.5651-2.9360.21811350.18926972832100
2.936-3.69770.21051330.17342741287499
3.6977-28.6420.18961390.16722866300599
Refinement TLS params.Method: refined / Origin x: 56.643 Å / Origin y: 72.2797 Å / Origin z: -2.2828 Å
111213212223313233
T0.2114 Å20.0133 Å2-0.0106 Å2-0.2685 Å2-0.0272 Å2--0.2358 Å2
L2.8434 °20.0705 °2-0.5496 °2-1.0392 °20.4389 °2--1.3972 °2
S-0.0795 Å °0.2158 Å °-0.1498 Å °-0.0142 Å °0.083 Å °-0.1773 Å °0.1516 Å °-0.1979 Å °0.0006 Å °
Refinement TLS groupSelection details: chain 'A' and (resseq 53:204)

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