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- PDB-2rld: CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM S23 RIB... -

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Database: PDB / ID: 2rld
TitleCRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM S23 RIBOSOMAL PROTEIN FAMILY (BT_0352) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.70 A RESOLUTION
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology23S rRNA-intervening sequence protein / 23S rRNA-intervening sequence superfamily / 23S rRNA-intervening sequence protein / 23S rRNA-intervening sequence / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (NP_809265.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,57326
Polymers71,3895
Non-polymers1,18421
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.238, 83.823, 63.923
Angle α, β, γ (deg.)90.000, 97.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1MSELYSAA1 - 1152 - 116
2MSETHRBB5 - 1166 - 117
3MSETHRCC1 - 1162 - 117
4ASPILEDD7 - 1148 - 115
5ASNTHREE8 - 1179 - 118
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A PENTAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Uncharacterized protein


Mass: 14277.750 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Species: Bacteroides thetaiotaomicron / Strain: VPI-5482, DSM 2079, NCTC 10582, E50 / Gene: NP_809265.1, BT_0352 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AAW0
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: NANODROP, 0.2M CaCl2, 20.0% PEG 3350, no Buffer pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9798, 0.9537, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.95371
30.97961
ReflectionResolution: 1.7→29.643 Å / Num. obs: 63158 / % possible obs: 96.2 % / Redundancy: 2 % / Biso Wilson estimate: 20.65 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.741.80.4411.7779142880.44188.2
1.74-1.791.90.3562.1830843420.35692.3
1.79-1.8420.2712.8870243660.27194.6
1.84-1.920.2013.8873142630.20196.2
1.9-1.962.10.1495875441830.14997
1.96-2.032.10.1216.1860740850.12197.1
2.03-2.112.10.0937.8823639190.09397.3
2.11-2.192.10.0769.3797637960.07697.6
2.19-2.292.10.06610.2762436510.06697.7
2.29-2.42.10.05911.7724034590.05997.9
2.4-2.532.10.05511.9693033260.05597.9
2.53-2.692.10.05312.4654531590.05398
2.69-2.872.10.04812.9605729390.04897.9
2.87-3.12.10.04214.5572427500.04297.2
3.1-3.420.0415.2516225230.0497.3
3.4-3.820.03615.6454522860.03697.6
3.8-4.391.90.03516.9371419740.03595.3
4.39-5.382.10.03615.5361617430.03699
5.38-7.62.10.04115288913660.04199.8
7.6-29.6432.10.03317.415517400.03396.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.643 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.051 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. EDO, CL AND CA MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3216 5.1 %RANDOM
Rwork0.163 ---
obs0.165 63130 95.92 %-
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: 17.012 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.19 Å2
2---0.29 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 69 518 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224733
X-RAY DIFFRACTIONr_bond_other_d0.0010.023232
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9666390
X-RAY DIFFRACTIONr_angle_other_deg0.89937939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3565601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27625.63238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3915920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6041529
X-RAY DIFFRACTIONr_chiral_restr0.0750.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
X-RAY DIFFRACTIONr_nbd_refined0.220.21188
X-RAY DIFFRACTIONr_nbd_other0.1780.23411
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22409
X-RAY DIFFRACTIONr_nbtor_other0.0840.22405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2409
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1480.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.225
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0490.21
X-RAY DIFFRACTIONr_mcbond_it1.66132941
X-RAY DIFFRACTIONr_mcbond_other0.61431150
X-RAY DIFFRACTIONr_mcangle_it2.20454646
X-RAY DIFFRACTIONr_scbond_it4.4181999
X-RAY DIFFRACTIONr_scangle_it6.586111718
Refine LS restraints NCS

Ens-ID: 1 / Number: 1200 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.630.5
2BMEDIUM POSITIONAL0.570.5
3CMEDIUM POSITIONAL0.530.5
4DMEDIUM POSITIONAL0.550.5
5EMEDIUM POSITIONAL0.50.5
1AMEDIUM THERMAL1.022
2BMEDIUM THERMAL1.152
3CMEDIUM THERMAL1.122
4DMEDIUM THERMAL1.252
5EMEDIUM THERMAL1.352
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 205 -
Rwork0.239 4072 -
all-4277 -
obs--87.93 %
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)
11.92370.0599-0.58051.141-0.12411.29210.01740.06930.04820.04810.09860.0582-0.08970.1144-0.116-0.034-0.0115-0.0102-0.0148-0.0052-0.026749.542941.808854.5057
21.72650.5280.7921.5231-0.00280.7888-0.01960.0383-0.0541-0.01780.0719-0.1332-0.1602-0.0177-0.0523-0.0198-0.02510.019-0.04610.0053-0.041934.40256.394463.4687
30.8304-0.29530.85221.335-0.57452.23880.08050.2040.0154-0.1549-0.1335-0.13920.07980.34680.053-0.02050.02450.0010.04610.0328-0.01547.185740.352731.0152
41.3657-0.1571-0.52881.785-0.1471.87480.0516-0.0450.20010.01670.0246-0.1632-0.18630.1319-0.0761-0.0287-0.022-0.0038-0.0489-0.0089-0.018732.232456.665524.7082
50.42430.0459-0.13741.76930.03481.13620.0115-0.0160.02280.0744-0.021-0.06430.012-0.0780.0095-0.05430.024-0.0008-0.04640.0147-0.058824.468766.106544.4964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1151 - 116
2X-RAY DIFFRACTION2BB5 - 1166 - 117
3X-RAY DIFFRACTION3CC1 - 1162 - 117
4X-RAY DIFFRACTION4DD7 - 1148 - 115
5X-RAY DIFFRACTION5EE8 - 1179 - 118

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