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- PDB-4myr: Crystal structure of a putative CpaE2 pilus assembly protein (Cpa... -

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Basic information

Entry
Database: PDB / ID: 4myr
TitleCrystal structure of a putative CpaE2 pilus assembly protein (CpaE2) from Sinorhizobium meliloti 1021 at 2.72 A resolution (PSI Community Target, Shapiro)
ComponentsCpaE2 pilus assembly protein
KeywordsTRANSCRIPTION / Response regulator receiver domain / PF00072 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


TadE-like / TadE-like protein / : / AAA domain / AAA domain / CheY-like superfamily / Response regulator / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CpaE2 pilus assembly protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative CpaE2 pilus assembly protein (CpaE2) from Sinorhizobium meliloti 1021 at 2.72 A resolution (PSI Community Target, Shapiro)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CpaE2 pilus assembly protein
B: CpaE2 pilus assembly protein
C: CpaE2 pilus assembly protein
D: CpaE2 pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)65,2914
Polymers65,2914
Non-polymers00
Water93752
1
A: CpaE2 pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)16,3231
Polymers16,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CpaE2 pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)16,3231
Polymers16,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CpaE2 pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)16,3231
Polymers16,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CpaE2 pilus assembly protein


Theoretical massNumber of molelcules
Total (without water)16,3231
Polymers16,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.013, 48.371, 73.869
Angle α, β, γ (deg.)108.230, 90.030, 97.400
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CpaE2 pilus assembly protein


Mass: 16322.695 Da / Num. of mol.: 4 / Fragment: UNP residues 30-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: cpaE2, RA0855, SMa1573 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q92YL8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (30-157) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30.00% MPD, 0.1M MES pH 6.0, NANODROP, 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: 0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.72→46.578 Å / Num. obs: 14731 / % possible obs: 88.1 % / Observed criterion σ(I): -3 / Redundancy: 3.58 % / Biso Wilson estimate: 72.89 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.72-2.823.620.68125492151689.4
2.82-2.930.47835249143689.9
2.93-3.060.33445140141388.9
3.06-3.220.2455.44706134281.4
3.22-3.420.1687.55116142086.6
3.42-3.690.10210.95600157092.3
3.69-4.060.0813.55225146990.1
4.06-4.640.05318.24750138284.8
4.64-5.820.04820.25154144388.6
5.82-46.5780.04424.45449150289

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n0p

4n0p


Resolution: 2.72→46.578 Å / Cor.coef. Fo:Fc: 0.9336 / Cor.coef. Fo:Fc free: 0.8851 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
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.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.253 746 5.06 %RANDOM
Rwork0.1948 ---
obs0.1976 14730 89.53 %-
Displacement parametersBiso max: 171.13 Å2 / Biso mean: 62.5658 Å2 / Biso min: 23.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0.9585 Å2-0.8055 Å2
2---9.5711 Å21.5807 Å2
3---9.5111 Å2
Refine analyzeLuzzati coordinate error obs: 0.437 Å
Refinement stepCycle: LAST / Resolution: 2.72→46.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 0 52 3706
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1767SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes551HARMONIC5
X-RAY DIFFRACTIONt_it3709HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4144SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3709HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5024HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion2.59
LS refinement shellResolution: 2.72→2.94 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.305 165 5.34 %
Rwork0.2276 2922 -
all0.2318 3087 -
obs--89.53 %
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)
13.0087-0.1762-0.38444.04450.77815.045-0.012-0.00560.01140.13990.1572-0.12060.44790.3677-0.1452-0.23620.0759-0.08290.03480.0575-0.111712.68310.269238.3117
26.22290.64690.37342.5194-0.2554.12380.0403-0.0199-0.3410.0086-0.1233-0.24230.24770.5490.083-0.25030.0713-0.0230.09010.1436-0.192920.357619.0416-2.3872
35.06230.4270.45522.94920.23024.456-0.0196-0.45990.32340.22540.09030.3033-0.2392-0.5685-0.0707-0.23560.07760.035-0.00250.1146-0.062434.219922.089537.5505
44.4411-0.26570.58134.0181.07775.1419-0.04310.36540.3282-0.14420.02720.0238-0.5955-0.23510.0159-0.159-0.0213-0.036-0.0850.1615-0.108441.924636.169411.3197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|30 - 152}A30 - 152
2X-RAY DIFFRACTION2{B|30 - 154}B30 - 154
3X-RAY DIFFRACTION3{C|30 - 155}C30 - 155
4X-RAY DIFFRACTION4{D|31 - 152}D31 - 152

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