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- PDB-2dhn: COMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AURE... -

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Basic information

Entry
Database: PDB / ID: 2dhn
TitleCOMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 2.2 A RESOLUTION
Components7,8-DIHYDRONEOPTERIN ALDOLASE
KeywordsPRODUCT COMPLEX / PTERINE BINDING / FOLATE BIOSYNTHESIS / ANTIBIOTIC TARGET / BETA-BARREL
Function / homology
Function and homology information


7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / isomerase activity / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PH2 / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.2 Å
AuthorsHennig, M. / D'Arcy, A. / Hampele, I.C. / Page, M.G.P. / Oefner, C.H. / Dale, G.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from Staphylococcus aureus.
Authors: Hennig, M. / D'Arcy, A. / Hampele, I.C. / Page, M.G. / Oefner, C. / Dale, G.E.
History
DepositionMar 31, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-DIHYDRONEOPTERIN ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,7701
Non-polymers1951
Water1,33374
1
A: 7,8-DIHYDRONEOPTERIN ALDOLASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)111,71916
Polymers110,1578
Non-polymers1,5618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area26350 Å2
ΔGint-80 kcal/mol
Surface area34030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.200, 62.200, 123.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 7,8-DIHYDRONEOPTERIN ALDOLASE / DHNA


Mass: 13769.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: DHNA / Plasmid: PSADHNA / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (PREP4) / References: UniProt: P56740
#2: Chemical ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.143.41
2
Crystal growpH: 6.6 / Details: pH 6.6
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1200 mMmagnesium formate1drop
2175 mMmagnesium formate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1997 / Details: MIRROR
RadiationMonochromator: SUPPER MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 27653 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.9 / % possible all: 98.6
Reflection
*PLUS
Num. obs: 6008 / Num. measured all: 27653

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement
Starting model: DHNA UNLIGANDED

Resolution: 2.2→30 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: RFREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -5 %RANDOM
Rwork0.202 ---
obs0.202 6008 95.9 %-
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 14 74 1055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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