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- PDB-4p53: ValA (2-epi-5-epi-valiolone synthase) from Streptomyces hygroscop... -

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Basic information

Entry
Database: PDB / ID: 4p53
TitleValA (2-epi-5-epi-valiolone synthase) from Streptomyces hygroscopicus subsp. jinggangensis 5008 with NAD+ and Zn2+ bound
ComponentsCyclase
KeywordsLYASE / sugar phosphate cyclase / pseudoglycoside / sedoheptulose 7-phosphate
Function / homology
Function and homology information


2-epi-5-epi-valiolone synthase / antibiotic biosynthetic process / lyase activity / nucleotide binding / metal ion binding
Similarity search - Function
3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 2-epi-5-epi-valiolone synthase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. jinggangensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKean, K.M. / Codding, S.J. / Karplus, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI061528 United States
CitationJournal: Biochemistry / Year: 2014
Title: Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus.
Authors: Kean, K.M. / Codding, S.J. / Asamizu, S. / Mahmud, T. / Karplus, P.A.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_symm_contact / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.dist / _software.classification / _struct_keywords.pdbx_keywords
Revision 1.3Dec 11, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_symm_contact ...pdbx_audit_support / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7414
Polymers45,9041
Non-polymers8373
Water3,387188
1
A: Cyclase
hetero molecules

A: Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4818
Polymers91,8072
Non-polymers1,6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area8860 Å2
ΔGint-103 kcal/mol
Surface area25690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.186, 77.186, 99.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-50-

PRO

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Components

#1: Protein Cyclase /


Mass: 45903.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus subsp. jinggangensis (bacteria)
Strain: 5008 / Gene: SHJG_0276 / Production host: Escherichia coli (E. coli) / References: UniProt: H2K887
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.73 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.6 M succinic acid, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2012
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→66.9 Å / Num. obs: 20232 / % possible obs: 99.4 % / Redundancy: 26.8 % / Biso Wilson estimate: 41.49 Å2 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 19.3 % / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLM1.0.7data reduction
SCALA2.0.6data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLH

3clh


Resolution: 2.1→66.845 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1036 5.13 %RANDOM
Rwork0.1789 ---
obs0.1829 20193 98.83 %-
all-2797 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: 1 / Resolution: 2.1→66.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 52 188 3025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012872
X-RAY DIFFRACTIONf_angle_d1.2593906
X-RAY DIFFRACTIONf_dihedral_angle_d13.9911067
X-RAY DIFFRACTIONf_chiral_restr0.051463
X-RAY DIFFRACTIONf_plane_restr0.006518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21080.34411650.27842616X-RAY DIFFRACTION97
2.2108-2.34940.32261570.26522650X-RAY DIFFRACTION98
2.3494-2.53080.30111330.2232717X-RAY DIFFRACTION99
2.5308-2.78550.31311240.21292754X-RAY DIFFRACTION99
2.7855-3.18850.2731700.19462720X-RAY DIFFRACTION99
3.1885-4.01710.24091430.15312778X-RAY DIFFRACTION100
4.0171-66.87880.22421440.1472922X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 29.4467 Å / Origin y: 45.4145 Å / Origin z: 30.8642 Å
111213212223313233
T0.2695 Å2-0.0028 Å20.0027 Å2-0.2369 Å2-0.0078 Å2--0.2553 Å2
L1.0811 °2-0.4575 °20.3295 °2-2.0113 °20.0936 °2--2.6116 °2
S0.1251 Å °0.1196 Å °-0.0933 Å °-0.3375 Å °-0.0484 Å °0.0165 Å °-0.0104 Å °0.3391 Å °-0.0653 Å °
Refinement TLS groupSelection details: chain A and (resid 26:398 )

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