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- PDB-4ae5: STRUCTURE OF A MAJOR REGULATOR OF STAPHYLOCOCCAL PATHOGENESIS -

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Basic information

Entry
Database: PDB / ID: 4ae5
TitleSTRUCTURE OF A MAJOR REGULATOR OF STAPHYLOCOCCAL PATHOGENESIS
ComponentsSIGNAL TRANSDUCTION PROTEIN TRAP
KeywordsSIGNALING PROTEIN / PHOSPHORYLATION / RNAIII / RAP / QUORUM SENSING / BIOFILM / TOXIN PRODUCTION
Function / homology
Function and homology information


heme oxygenase (decyclizing) activity / heme catabolic process / membrane
Similarity search - Function
: / ABM domain profile. / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Signal transduction protein TRAP / Signal transduction protein TRAP
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsHirshberg, M. / Henrick, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the Signal Transduction Protein Trap (Target of Rnaiii-Activating Protein).
Authors: Henrick, K. / Hirshberg, M.
History
DepositionJan 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL TRANSDUCTION PROTEIN TRAP
B: SIGNAL TRANSDUCTION PROTEIN TRAP
C: SIGNAL TRANSDUCTION PROTEIN TRAP
D: SIGNAL TRANSDUCTION PROTEIN TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4838
Polymers78,2994
Non-polymers1844
Water4,720262
1
A: SIGNAL TRANSDUCTION PROTEIN TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6212
Polymers19,5751
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SIGNAL TRANSDUCTION PROTEIN TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6212
Polymers19,5751
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SIGNAL TRANSDUCTION PROTEIN TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6212
Polymers19,5751
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SIGNAL TRANSDUCTION PROTEIN TRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6212
Polymers19,5751
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.076, 70.868, 79.082
Angle α, β, γ (deg.)90.00, 111.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SIGNAL TRANSDUCTION PROTEIN TRAP / TARGET OF RNAIII-ACTIVATING PROTEIN


Mass: 19574.729 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: RN6390B / References: UniProt: Q7A4W3, UniProt: Q2G2F3*PLUS
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.3 Å3/Da / Density % sol: 46.55 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.66
Details: HANGING DROP, 18 DEGREES CELCIUS, 18% PEG 4K, 0.050 M NACIT PH 5.66, 1% PEG 500 MME, PROTEIN IN DROP 4.4MG/ML DROP 1:1, CRYOPROTECTANT USED: 20% PEG 4K, 0.050 M NA CITRATE PH 5.66, 1% PEG 500 MME, 35% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.2445
DetectorType: ADSC CCD / Detector: CCD / Date: May 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2445 Å / Relative weight: 1
ReflectionResolution: 1.85→74.5 Å / Num. obs: 60732 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.23 / % possible all: 79.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.09 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.25957 2846 5.1 %RANDOM
Rwork0.21109 ---
obs0.21358 53021 91.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.972 Å20 Å20.706 Å2
2---0.032 Å20 Å2
3----0.421 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 12 262 5582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.025589
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9257560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65523.257304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47715906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5621522
X-RAY DIFFRACTIONr_chiral_restr0.1440.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214410
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.22393
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23750
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9751.855598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9852.737550
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3495.5671886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0159.0096494
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 174 -
Rwork0.232 3290 -
obs--78.78 %
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)
10.953-0.0597-0.28130.629-0.55981.86190.0160.0651-0.04910.07810.0729-0.0083-0.0452-0.11720.01620.0344-0.0134-0.0090.03250.00290.04265.66533.01814.014
20.7280.11260.14430.70.01980.97920.00580.0091-0.01490.0202-0.04750.03810.0361-0.0323-0.04960.015-0.0007-0.01750.0080.01080.049824.0633.28739.738
32.65290.7305-1.01381.56080.04932.3068-0.0749-0.1060.0311-0.205-0.11890.0489-0.05140.0816-0.03340.0501-0.02180.01640.0269-0.00070.030845.79432.0875.705
41.5607-0.3321-0.41920.57310.21851.27040.0026-0.11150.1089-0.1256-0.01610.01130.02350.16750.23910.04540.03090.01660.09950.03140.05252.39831.85448.106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 2066
2X-RAY DIFFRACTION2B1 - 2111
3X-RAY DIFFRACTION3C2 - 2024
4X-RAY DIFFRACTION4D2 - 2061

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