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- PDB-4iaj: Crystal structure of a conserved domain protein (SP_1775) from St... -

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Basic information

Entry
Database: PDB / ID: 4iaj
TitleCrystal structure of a conserved domain protein (SP_1775) from Streptococcus pneumoniae TIGR4 at 1.91 A resolution
ComponentsConserved domain protein
KeywordsStructural Genomics / Unknown Function / DUF4649 / PF15507 family protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4649 / Protein of unknown function DUF4649 / Domain of unknown function (DUF4649) / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta / Unknown ligand / Conserved domain protein / Conserved domain protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a conserved domain protein (SP_1775) from Streptococcus pneumoniae TIGR4 at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: Conserved domain protein
B: Conserved domain protein
C: Conserved domain protein
D: Conserved domain protein
E: Conserved domain protein
F: Conserved domain protein
G: Conserved domain protein
H: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,35333
Polymers73,7838
Non-polymers56925
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16180 Å2
ΔGint-78 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.152, 98.168, 68.930
Angle α, β, γ (deg.)90.000, 107.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52E
62F
72G
82H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A25 - 100
2116B25 - 100
3116C25 - 100
4116D25 - 100
5116E25 - 100
6116F25 - 100
7116G25 - 100
8116H25 - 100
1124A101 - 201
2124B101 - 201
3124C101 - 201
4124D101 - 201
5124E101 - 201
6124F101 - 201
7124G101 - 201
8124H101 - 201

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Conserved domain protein


Mass: 9222.898 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: NP_346208.1, SP_1775 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q97P69, UniProt: A0A0H2UR98*PLUS

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Non-polymers , 5 types, 334 molecules

#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 9 / Source method: obtained synthetically
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 24-100) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 24-100) WAS EXPRESSED WITH AN N-TERMINAL 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium nitrate, 20.0% polyethylene glycol 3350, NANODROP, 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: 0.918401,0.979338,0.979111
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.9793381
30.9791111
ReflectionResolution: 1.91→29.304 Å / Num. obs: 48771 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.14 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.91-1.980.5641.515463949395.4
1.98-2.060.3662.115407944895.9
2.06-2.150.2772.714550893895.8
2.15-2.260.2083.814958920796.3
2.26-2.410.1515.116224998096.8
2.41-2.590.17.414750908096.6
2.59-2.850.0699.915379950097.1
2.85-3.260.0416.115160938296.4
3.26-4.10.02325.514899932195.4
4.10.01732.415278950495.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→29.304 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.466 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.158
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 RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.MAGNESIUM (MG) AND 1,2-ETHANEDIOL FROM THE CRYSTALLIZATION/CRYO CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 6. UNKNOWN LIGANDS (UNL) AND UNKNOWN ATOMS (UNX) HAVE BEEN MODELED INTO DIFFERENCE ELECTRON DENSITY WITHIN A CHANNEL FORMED BY THE OCTAMERIC ASSEMBLY IN THE ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 2471 5.1 %RANDOM
Rwork0.1798 ---
obs0.1824 48740 98.58 %-
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: 100.42 Å2 / Biso mean: 36.0527 Å2 / Biso min: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å2-0.35 Å2
2--1.4 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.91→29.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 87 309 5376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025449
X-RAY DIFFRACTIONr_bond_other_d0.0010.024869
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9567394
X-RAY DIFFRACTIONr_angle_other_deg0.6713.00111221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3535667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9625.048315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78715874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0361518
X-RAY DIFFRACTIONr_chiral_restr0.0440.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021377
X-RAY DIFFRACTIONr_mcbond_it2.2493.7382483
X-RAY DIFFRACTIONr_mcbond_other2.2493.7362482
X-RAY DIFFRACTIONr_mcangle_it3.2016.9553115
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A912LOOSE POSITIONAL0.45
1B912LOOSE POSITIONAL0.635
1C912LOOSE POSITIONAL0.445
1D912LOOSE POSITIONAL0.495
1E912LOOSE POSITIONAL0.515
1F912LOOSE POSITIONAL0.35
1G912LOOSE POSITIONAL0.625
1H912LOOSE POSITIONAL0.415
1A912LOOSE THERMAL5.8310
1B912LOOSE THERMAL4.7610
1C912LOOSE THERMAL8.410
1D912LOOSE THERMAL4.6510
1E912LOOSE THERMAL3.9910
1F912LOOSE THERMAL5.310
1G912LOOSE THERMAL5.7610
1H912LOOSE THERMAL4.6510
2A5MEDIUM POSITIONAL0.210.2
2B5MEDIUM POSITIONAL0.030.2
2C5MEDIUM POSITIONAL0.040.2
2D5MEDIUM POSITIONAL0.270.2
2E5MEDIUM POSITIONAL0.20.2
2F5MEDIUM POSITIONAL0.150.2
2G5MEDIUM POSITIONAL0.180.2
2H5MEDIUM POSITIONAL0.190.2
2A5MEDIUM THERMAL4.7810
2B5MEDIUM THERMAL3.7410
2C5MEDIUM THERMAL4.9110
2D5MEDIUM THERMAL3.1710
2E5MEDIUM THERMAL3.710
2F5MEDIUM THERMAL5.8910
2G5MEDIUM THERMAL5.0810
2H5MEDIUM THERMAL5.8610
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 172 -
Rwork0.266 3390 -
all-3562 -
obs--97.56 %
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)
11.21020.1395-0.83830.98110.05753.12580.04460.18060.0309-0.23330.0175-0.0021-0.0390.1108-0.06210.1113-0.02220.00920.1216-0.00270.10814.56614.344826.4161
20.7927-0.3068-0.57162.44960.3251.2657-0.03230.159-0.2468-0.2371-0.008-0.10230.21890.04940.04030.1047-0.005-0.01710.1038-0.05550.1292-0.732-4.525631.3669
30.878-0.09850.02770.51070.0613.22220.037-0.1229-0.03960.12590.01360.0172-0.0461-0.0011-0.05060.0916-0.012-0.00690.12360.00190.11497.674218.984465.385
42.46360.32730.18112.6960.02311.1605-0.00390.04470.4778-0.0097-0.02030.2613-0.4295-0.0720.02420.1742-0.0017-0.00570.07170.0250.12134.865735.072942.7868
53.3836-0.53040.20042.3615-0.01531.32680.07610.1402-0.5302-0.054-0.0152-0.08610.48720.2587-0.06090.18050.0924-0.01690.0975-0.0090.129717.0322-1.873749.213
61.49620.2382-0.25012.1569-0.76973.45760.138-0.3231-0.28340.3213-0.03790.0870.5015-0.0851-0.10010.1813-0.0583-0.01750.08340.04540.122-5.8337-1.959259.0142
72.17440.06581.10022.1224-0.68912.0988-0.02310.25760.1391-0.1829-0.04930.108-0.21380.07020.07240.0893-0.0016-0.02510.1079-0.00390.0915-10.082321.266728.1879
83.3502-0.1164-0.10413.02290.382.1039-0.0406-0.13650.47510.31820.06490.3089-0.4417-0.3861-0.02420.14910.09340.03510.11790.01290.12-14.509624.241855.6801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 100
2X-RAY DIFFRACTION2B24 - 100
3X-RAY DIFFRACTION3C26 - 100
4X-RAY DIFFRACTION4D26 - 99
5X-RAY DIFFRACTION5E27 - 99
6X-RAY DIFFRACTION6F27 - 99
7X-RAY DIFFRACTION7G27 - 99
8X-RAY DIFFRACTION8H26 - 100

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