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- PDB-1npy: Structure of shikimate 5-dehydrogenase-like protein HI0607 -

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Basic information

Entry
Database: PDB / ID: 1npy
TitleStructure of shikimate 5-dehydrogenase-like protein HI0607
ComponentsHypothetical shikimate 5-dehydrogenase-like protein HI0607
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / NADP binding / cytosol
Similarity search - Function
Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / Shikimate dehydrogenase-like protein HI_0607
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKorolev, S. / Koroleva, O. / Zarembinski, T. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of a Novel Shikimate Dehydrogenase from Haemophilus influenzae.
Authors: Singh, S. / Korolev, S. / Koroleva, O. / Zarembinski, T. / Collart, F. / Joachimiak, A. / Christendat, D.
History
DepositionJan 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical shikimate 5-dehydrogenase-like protein HI0607
B: Hypothetical shikimate 5-dehydrogenase-like protein HI0607
C: Hypothetical shikimate 5-dehydrogenase-like protein HI0607
D: Hypothetical shikimate 5-dehydrogenase-like protein HI0607
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9987
Polymers119,8664
Non-polymers1323
Water20,6991149
1
A: Hypothetical shikimate 5-dehydrogenase-like protein HI0607


Theoretical massNumber of molelcules
Total (without water)29,9661
Polymers29,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical shikimate 5-dehydrogenase-like protein HI0607
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0102
Polymers29,9661
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical shikimate 5-dehydrogenase-like protein HI0607
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0102
Polymers29,9661
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical shikimate 5-dehydrogenase-like protein HI0607
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0102
Polymers29,9661
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.578, 66.575, 96.916
Angle α, β, γ (deg.)90.00, 109.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical shikimate 5-dehydrogenase-like protein HI0607


Mass: 29966.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0607 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: P44774
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: NaCl, NaAcetate, PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
20.1 Msodium acetate1reservoirpH4.6
32.0 M1reservoirNaCl
410 %(v/v)PEG4001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97921, 0.97935
SYNCHROTRONAPS 19-ID20.97892
Detector
TypeIDDetectorDate
SBC-21CCDJul 2, 2002
SBC-22CCDFeb 13, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979351
30.978921
ReflectionResolution: 1.75→50 Å / Num. all: 109795 / Num. obs: 108148 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 88
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.214 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21908 5397 5 %RANDOM
Rwork0.17934 ---
obs0.1813 102713 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.535 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.23 Å2
2--0.42 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8363 0 9 1149 9521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228534
X-RAY DIFFRACTIONr_bond_other_d0.0020.027769
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.94511531
X-RAY DIFFRACTIONr_angle_other_deg0.884318063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07351075
X-RAY DIFFRACTIONr_chiral_restr0.1050.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029551
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021741
X-RAY DIFFRACTIONr_nbd_refined0.2330.21694
X-RAY DIFFRACTIONr_nbd_other0.2510.29139
X-RAY DIFFRACTIONr_nbtor_other0.0860.24888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2732
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.2142
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.292
X-RAY DIFFRACTIONr_mcbond_it1.0561.55359
X-RAY DIFFRACTIONr_mcangle_it1.87728586
X-RAY DIFFRACTIONr_scbond_it3.22133175
X-RAY DIFFRACTIONr_scangle_it5.3274.52945
LS refinement shellResolution: 1.749→1.794 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 350
Rwork0.22 6498
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.8 Å / Rfactor Rwork: 0.22

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