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- PDB-2rcd: CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3225... -

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Basic information

Entry
Database: PDB / ID: 2rcd
TitleCRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3225 FAMILY (ECA3500) FROM PECTOBACTERIUM ATROSEPTICUM SCRI1043 AT 2.32 A RESOLUTION
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyAtzH-like / AtzH-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_051588.1) from Erwinia carotovora subsp. atroseptica SCRI1043 at 2.32 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: 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: 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 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8498
Polymers58,7074
Non-polymers1424
Water1,964109
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4244
Polymers29,3532
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
MethodPISA
2
C: Uncharacterized protein
hetero molecules

C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4244
Polymers29,3532
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_754-x+2,y,-z-11
3
D: Uncharacterized protein
hetero molecules

D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4244
Polymers29,3532
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Unit cell
Length a, b, c (Å)93.375, 93.524, 72.919
Angle α, β, γ (deg.)90.000, 105.320, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 0 - 127 / Label seq-ID: 1 - 128

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Uncharacterized protein


Mass: 14676.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Species: Pectobacterium atrosepticum / Strain: SCRI 1043 / Gene: YP_051588.1, ECA3500 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6D1E8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 1.1M Lithium chloride, 24.0% PEG 6000, 0.1M HEPES pH 7.5, 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: 0.97898 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 26, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.32→29.463 Å / Num. obs: 25597 / % possible obs: 97.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 38.72 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.32-2.383.20.6391.1611418910.63997
2.38-2.453.20.5331.3587018110.53396.9
2.45-2.523.20.5281.4572417790.52897.1
2.52-2.593.20.4191.7558017260.41997.2
2.59-2.683.20.3282.3544916850.32897.5
2.68-2.773.20.2463523116150.24697.4
2.77-2.883.20.2313.2507415680.23197.6
2.88-33.20.1784.1488215200.17897.8
3-3.133.20.1285.7467914530.12897.7
3.13-3.283.20.1016.9449413930.10197.9
3.28-3.463.20.0828.4428113370.08298.3
3.46-3.673.20.0798.8401012560.07998.3
3.67-3.923.20.079.7370811610.0798.3
3.92-4.243.20.0611358611190.0698.4
4.24-4.643.20.05610.8325210280.05698.3
4.64-5.193.20.0610.328719100.0698.3
5.19-5.993.10.06410.925658210.06498.6
5.99-7.3430.06810.121036960.06898.8
7.34-10.3830.05411.915765320.05498.6
10.38-29.4632.80.05411.68382960.05494.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.32→29.463 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.796 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.237
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 RESIDUAL B FACTORS ONLY. 4. CHLORIDE ANIONS FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1291 5 %RANDOM
Rwork0.187 ---
obs0.19 25596 97.53 %-
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 mean: 43.889 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20.93 Å2
2---3.3 Å20 Å2
3---4.94 Å2
Refinement stepCycle: LAST / Resolution: 2.32→29.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 4 109 4082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224064
X-RAY DIFFRACTIONr_bond_other_d0.0020.022678
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9335521
X-RAY DIFFRACTIONr_angle_other_deg1.02936450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.285512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.27722.593189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05115644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9511540
X-RAY DIFFRACTIONr_chiral_restr0.0940.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
X-RAY DIFFRACTIONr_nbd_refined0.190.3749
X-RAY DIFFRACTIONr_nbd_other0.1850.32761
X-RAY DIFFRACTIONr_nbtor_refined0.180.51967
X-RAY DIFFRACTIONr_nbtor_other0.0870.52225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.5268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.327
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.522
X-RAY DIFFRACTIONr_mcbond_it1.63532605
X-RAY DIFFRACTIONr_mcbond_other0.44831051
X-RAY DIFFRACTIONr_mcangle_it2.29854045
X-RAY DIFFRACTIONr_scbond_it4.68681702
X-RAY DIFFRACTIONr_scangle_it5.854111475
Refine LS restraints NCS

Ens-ID: 1 / Number: 1612 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.180.5
2BMEDIUM POSITIONAL0.240.5
3CMEDIUM POSITIONAL0.170.5
4DMEDIUM POSITIONAL0.20.5
1AMEDIUM THERMAL0.772
2BMEDIUM THERMAL0.772
3CMEDIUM THERMAL0.712
4DMEDIUM THERMAL0.642
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 87 -
Rwork0.263 1797 -
all-1884 -
obs--96.71 %
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)
12.3916-0.224-0.70028.225-0.65673.41970.01870.1173-0.0657-0.7947-0.07150.16680.08070.00740.05280.07-0.00110.0144-0.1459-0.02-0.32192.626454.155-75.4621
21.5110.27761.03067.3785-0.69043.51640.09250.00340.09630.0212-0.11090.0687-0.225-0.03250.0183-0.06560.00530.0209-0.1422-0.0113-0.246192.608169.25-65.5311
35.49610.1714-0.75561.63431.11773.25-0.11830.11430.1716-0.10330.06380.156-0.0027-0.1530.0545-0.18240.0034-0.0252-0.08630.0179-0.168395.460971.8314-40.1304
48.34530.42340.97580.8931-1.11932.9641-0.06890.6316-0.4573-0.0320.12110.0066-0.0480.1072-0.0523-0.1751-0.0056-0.00810.0281-0.0466-0.019863.738778.7792-40.1934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1271 - 128
2X-RAY DIFFRACTION2BB0 - 1271 - 128
3X-RAY DIFFRACTION3CC0 - 1271 - 128
4X-RAY DIFFRACTION4DD0 - 1271 - 128

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