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- PDB-4cr8: Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with NAD -

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Basic information

Entry
Database: PDB / ID: 4cr8
TitleCrystal structure of the N-acetyl-D-mannosamine dehydrogenase with NAD
ComponentsN-ACYLMANNOSAMINE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / SUBSTRATE SELECTIVITY
Function / homology
Function and homology information


N-acylmannosamine 1-dehydrogenase / N-acylmannosamine 1-dehydrogenase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / N-acylmannosamine 1-dehydrogenase
Similarity search - Component
Biological speciesFLAVOBACTERIUM SP. 141-8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGil-Ortiz, F. / Sola-Carvajal, A. / Garcia-Carmona, F. / Sanchez-Ferrer, A. / Rubio, V.
CitationJournal: Biochem.J. / Year: 2014
Title: Crystal Structures and Functional Studies Clarify Substrate Selectivity and Catalytic Residues for the Unique Orphan Enzyme N-Acetyl-D-Mannosamine Dehydrogenase.
Authors: Sola-Carvajal, A. / Gil-Ortiz, F. / Garcia-Carmona, F. / Rubio, V. / Sanchez-Ferrer, A.
History
DepositionFeb 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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: AUTHOR PROVIDED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
B: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
C: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
D: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
E: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
F: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
G: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
H: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,27016
Polymers219,9638
Non-polymers5,3078
Water11,620645
1
A: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
B: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules

A: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
B: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6358
Polymers109,9814
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area21330 Å2
ΔGint-127.8 kcal/mol
Surface area31850 Å2
MethodPISA
2
C: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
D: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
E: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
F: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6358
Polymers109,9814
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21330 Å2
ΔGint-131 kcal/mol
Surface area31480 Å2
MethodPISA
3
G: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules

G: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3184
Polymers54,9912
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5040 Å2
ΔGint-27.6 kcal/mol
Surface area21330 Å2
MethodPISA
4
H: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules

H: N-ACYLMANNOSAMINE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3184
Polymers54,9912
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5030 Å2
ΔGint-28 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.950, 146.787, 90.418
Angle α, β, γ (deg.)90.00, 115.29, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 500
2113B1 - 500
3113C1 - 500
4113D1 - 500
5113E1 - 500
6113F1 - 500
7113G1 - 500
8113H1 - 500

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.513577, 0.002176, -0.858041), (0.004045, -0.999992, -0.000115), (-0.858034, -0.003412, -0.513582)25.70291, -27.41414, 45.21368
3given(0.996746, -0.063939, 0.049083), (0.065553, 0.997336, -0.032005), (-0.046906, 0.035119, 0.998282)-27.41945, 38.62366, -38.7781
4given(0.556061, -0.059847, -0.828984), (-0.060203, -0.997684, 0.031643), (-0.828958, 0.032312, -0.558376)44.74463, -66.16026, 88.78649
5given(-0.997174, 0.058384, -0.047277), (0.059566, 0.997936, -0.023991), (0.045779, -0.026739, -0.998594)-11.57774, 37.96485, 120.85918
6given(-0.553943, 0.06063, 0.830344), (-0.064826, -0.997458, 0.029585), (0.830027, -0.03744, 0.556465)-83.39465, -65.94827, -7.18995
7given(0.994392, -0.00145, 0.10575), (0.001562, 0.999998, -0.000974), (-0.105749, 0.001134, 0.994392)-4.54399, 72.36591, -1.73002
8given(-0.598688, 0.004464, 0.80097), (-0.003033, -0.99999, 0.003306), (0.800977, -0.00045, 0.598695)-15.91742, -26.40263, -31.80527

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Components

#1: Protein
N-ACYLMANNOSAMINE 1-DEHYDROGENASE / NAMDH / N-ACETYL-D-MANNOSAMINE DEHYDROGENASE


Mass: 27495.346 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FLAVOBACTERIUM SP. 141-8 (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA2
References: UniProt: P22441, N-acylmannosamine 1-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.17 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8 / Details: 8 % (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 89504 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D1Y

2d1y


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.344 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25335 4723 5 %RANDOM
Rwork0.22186 ---
obs0.22347 89504 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.997 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.3 Å2
2---0.07 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14725 0 216 645 15586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915145
X-RAY DIFFRACTIONr_bond_other_d0.0040.029800
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.99420598
X-RAY DIFFRACTIONr_angle_other_deg1.093.00423802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26152092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16422.68541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.523152208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.95315146
X-RAY DIFFRACTIONr_chiral_restr0.0990.22428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117489
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023081
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1479loose positional0.055
2B1479loose positional0.045
3C1479loose positional0.045
4D1479loose positional0.045
5E1479loose positional0.045
6F1479loose positional0.045
7G1479loose positional0.045
8H1479loose positional0.055
1A1518tight thermal1.780.5
2B1518tight thermal1.830.5
3C1518tight thermal1.720.5
4D1518tight thermal2.110.5
5E1518tight thermal2.210.5
6F1518tight thermal1.770.5
7G1518tight thermal2.070.5
8H1518tight thermal1.680.5
1A1479loose thermal1.9810
2B1479loose thermal2.1510
3C1479loose thermal2.0110
4D1479loose thermal2.5210
5E1479loose thermal2.7210
6F1479loose thermal2.2110
7G1479loose thermal2.610
8H1479loose thermal2.2510
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 331 -
Rwork0.252 6451 -
obs--99.09 %

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