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- PDB-1bwd: INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE STRB1 FROM STREPTOMYCES GRISEUS -

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Basic information

Entry
Database: PDB / ID: 1bwd
TitleINOSAMINE-PHOSPHATE AMIDINOTRANSFERASE STRB1 FROM STREPTOMYCES GRISEUS
ComponentsPROTEIN (INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE)
KeywordsTRANSFERASE / AMIDINOTRANSFERASE / STREPTOMYCIN
Function / homologyscyllo-inosamine-4-phosphate amidinotransferase / scyllo-inosamine-4-phosphate amidinotransferase activity / streptomycin biosynthetic process / Glycine/inosamine-phosphate amidinotransferase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / Inosamine-phosphate amidinotransferase 1
Function and homology information
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFritsche, E. / Bergner, A. / Humm, A. / Piepersberg, W. / Huber, R.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus: an enzyme involved in streptomycin biosynthesis.
Authors: Fritsche, E. / Bergner, A. / Humm, A. / Piepersberg, W. / Huber, R.
History
DepositionSep 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Dec 11, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_ref_seq_dif.details
Revision 1.5Nov 3, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE)
B: PROTEIN (INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)77,4772
Polymers77,4772
Non-polymers00
Water00
1
A: PROTEIN (INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE)

B: PROTEIN (INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)77,4772
Polymers77,4772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_764-x+2,-y+1,z-1/21
Buried area3120 Å2
ΔGint-16 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.300, 121.300, 63.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.850824, 0.453596, -0.265231), (0.441441, -0.343264, 0.829035), (0.285003, -0.822448, -0.492294)
Vector: -25.3377, 32.2698, 32.6707)

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Components

#1: Protein PROTEIN (INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE) / E.C.2.1.4.2 TRANSFERASE / ADT


Mass: 38738.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: STRB1 / Plasmid: PRSET-STRB1 / Gene (production host): STRB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3PLYSS
References: UniProt: P08078, scyllo-inosamine-4-phosphate amidinotransferase

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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: 2.92 Å3/Da / Density % sol: 58 %
Crystal growpH: 5
Details: 20% PEG 4000, 0.1 M SODIUM CITRAT BUFFER (PH 5.0), 0.2 M AMMONIUM ACETATE
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.3 mg/mlprotein1drop
250 mMTris-HCl1drop
31 mMglutathione1drop
40.2 mMEDTA1drop
520 %(w/v)PEG40001reservoir
60.1 Msodium citrate1reservoir
70.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 14273 / % possible obs: 85.6 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rsym value: 0.144
Reflection shellResolution: 3.1→3.21 Å / Rsym value: 0.345 / % possible all: 75.3
Reflection
*PLUS
Num. measured all: 37728 / Rmerge(I) obs: 0.144
Reflection shell
*PLUS
% possible obs: 75.3 % / Rmerge(I) obs: 0.345

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1JDW

1jdw


Resolution: 3.1→10 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 --RANDOM
Rwork0.197 ---
obs-12488 86 %-
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5455 0 0 0 5455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.023
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.3

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