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- PDB-6ncs: Crystal structure of N-acetylneuraminic acid (Sialic acid) synthe... -

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Basic information

Entry
Database: PDB / ID: 6ncs
TitleCrystal structure of N-acetylneuraminic acid (Sialic acid) synthetase from Leptospira borgpetersenii serovar Hardjo-bovis in complex with citrate
ComponentsN-acetylneuraminic acid (Sialic acid) synthetase
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / N-acetylneuraminic acid synthase / Sialic acid synthetase / Leptospira borgpetersenii / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


carbohydrate biosynthetic process / catalytic activity
Similarity search - Function
N-acetylneuraminic acid synthase, N-terminal / NeuB family / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / FORMIC ACID / IODIDE ION / : / D(-)-TARTARIC ACID / N-acetylneuraminic acid (Sialic acid) synthetase
Similarity search - Component
Biological speciesLeptospira borgpetersenii serovar Hardjo-bovis
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of N-acetylneuraminic acid (Sialic acid) synthetase from Leptospira borgpetersenii serovar Hardjo-bovis in complex with citrate
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylneuraminic acid (Sialic acid) synthetase
B: N-acetylneuraminic acid (Sialic acid) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,86029
Polymers64,5722
Non-polymers3,28727
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-35 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.880, 49.120, 88.850
Angle α, β, γ (deg.)90.000, 112.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-acetylneuraminic acid (Sialic acid) synthetase


Mass: 32286.080 Da / Num. of mol.: 2 / Fragment: LpboA.19655.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197) (bacteria)
Strain: JB197 / Gene: LBJ_1133 / Plasmid: LpboA.19655.b.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q04TM5

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Non-polymers , 7 types, 545 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen, condition G8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM each: sodium formate, ammonium acetate, trisodium citrate, sodium potassium L- ...Details: Molecular Dimensions Morpheus screen, condition G8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM each: sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate: 100mM MOPS/HEPES-Na pH 7.5: LpboA.19655.b.B1.PS38488 at 22.9mg/ml. For phasing, the crystal was incubated for 20sec in reservoir solution with additional 10% of 5M NaI in ethylene glycol (500mM final concentration). Cryo: direct: tray: 303852g8: puck hyz8-5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 10, 2017 / Details: RIGAKU VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→43.375 Å / Num. obs: 50583 / % possible obs: 97.1 % / Redundancy: 10.241 % / Biso Wilson estimate: 26.797 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Χ2: 1.03 / Net I/σ(I): 25 / Num. measured all: 517998 / Scaling rejects: 470
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.856.7280.3984.2333810.9410.42888.2
1.85-1.96.7640.3444.9933830.9620.37190.1
1.9-1.956.7310.2636.6733610.9760.28492.9
1.95-2.016.9360.1998.2433280.9850.21495.1
2.01-2.086.8830.16710.4233310.9880.1896.9
2.08-2.157.9160.13813.0832280.9930.14798.4
2.15-2.239.160.11916.1831830.9950.12799.1
2.23-2.329.5450.10119.6830690.9960.10799.5
2.32-2.4310.260.09221.5729280.9970.09799.5
2.43-2.5510.8840.08124.7128020.9980.08599.5
2.55-2.6811.6920.07528.126920.9980.07999.8
2.68-2.8513.6320.06634.5425270.9990.06899.9
2.85-3.0414.7580.05740.5324100.9990.05999.8
3.04-3.2914.8060.05346.0522370.9990.05599.9
3.29-3.614.7490.04652.8420430.9990.04799.9
3.6-4.0214.4720.0457.8618790.9990.04199.9
4.02-4.6514.5060.03860.59165510.03999.6
4.65-5.6914.2860.04158.814150.9990.04399.7
5.69-8.0513.6530.04653.7510990.9990.04899.8
8.05-43.37512.7040.03762.586320.9990.03998.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_3339refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→43.375 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.82
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 2017 3.99 %0
Rwork0.1556 ---
obs0.1573 50574 97.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.63 Å2 / Biso mean: 24.9485 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.8→43.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 68 524 4929
Biso mean--48.39 34.24 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064569
X-RAY DIFFRACTIONf_angle_d0.8246218
X-RAY DIFFRACTIONf_dihedral_angle_d13.2042842
X-RAY DIFFRACTIONf_chiral_restr0.056722
X-RAY DIFFRACTIONf_plane_restr0.005817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.23871440.18353120326488
1.845-1.89490.24641490.1773203335290
1.8949-1.95070.19531250.17213286341193
1.9507-2.01360.20311530.16113333348695
2.0136-2.08560.2231390.15713470360997
2.0856-2.16910.18481340.1533501363599
2.1691-2.26780.19391390.15583517365699
2.2678-2.38740.21461450.158135363681100
2.3874-2.53690.21021420.166835643706100
2.5369-2.73280.22711300.167635883718100
2.7328-3.00770.21051510.168335693720100
3.0077-3.44280.18991740.156135633737100
3.4428-4.33690.16551650.132335783743100
4.3369-43.38760.19441270.149337293856100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.96550.4493-0.56211.10220.64371.91830.0460.0809-0.022-0.15630.024-0.0475-0.0110.0042-0.02370.230.02310.0060.07860.00410.137539.666515.320340.8803
24.9075-0.29481.71431.5921-0.4564.7357-0.06150.44760.0117-0.4432-0.0104-0.2893-0.10880.37670.13250.2926-0.01080.09070.11970.01270.174748.792817.199132.6096
32.95131.74320.41882.07631.13592.0714-0.03610.13-0.1135-0.33170.0516-0.0631-0.0922-0.073-0.03820.25380.03720.01850.10110.00710.131739.93038.213235.0275
43.83860.03960.27341.12690.52863.0539-0.00250.0417-0.3124-0.20010.04750.00140.1944-0.21880.0110.228-0.0131-0.02780.0706-0.00910.145632.29932.733737.5676
53.1232-0.4657-0.53611.57350.57432.51380.05730.1335-0.1695-0.2653-0.16820.2106-0.0252-0.35080.08260.17530.0025-0.0380.1203-0.00940.098226.93646.823446.6198
60.97210.4214-0.09231.7529-1.88412.24840.0989-0.00730.2861-0.3408-0.10050.0839-0.3771-0.2641-0.08630.3380.07290.01190.04950.01940.150433.348923.122746.3083
74.42223.6774-4.76754.5883-5.3677.69570.0494-0.16190.0908-0.1253-0.0418-0.0037-0.15720.1423-0.02640.13330.01040.00640.0942-0.03650.114338.507421.034657.7682
81.95620.106-0.58250.97770.32637.4862-0.0844-0.2975-0.17020.1572-0.0608-0.00820.32830.2670.15720.12460.0246-0.0240.15670.06560.184732.29047.785285.271
90.4501-0.431-0.61880.69280.60260.85650.03790.2789-0.2803-0.0047-0.28650.38170.2886-0.65770.28810.2012-0.0641-0.02640.3773-0.12440.272312.096612.755868.965
103.3783-0.66112.06171.34170.15755.99090.0892-0.15980.27370.0885-0.06230.0663-0.2636-0.15090.01020.096-0.00030.02790.2059-0.06170.17313.782631.491584.2718
111.9971-0.708-0.26931.43630.14590.9414-0.0546-0.2677-0.13640.1672-0.00260.1410.0532-0.14060.05520.1005-0.0356-00.2104-0.00940.121417.07813.892485.382
124.03860.387-0.75923.0181-1.04122.00640.03290.2943-0.3683-0.1552-0.18150.1750.3047-0.27610.09910.1059-0.0143-0.01440.139-0.04790.110423.55356.962469.3703
131.2685-0.2480.21612.82892.7254.42120.0632-0.08320.15940.0251-0.0977-0.00930.0031-0.04960.02780.057-0.00380.00110.1275-0.02120.101724.872424.683275.6354
140.3227-0.9697-0.74317.67265.82354.41810.03130.00340.0117-0.2068-0.18940.1674-0.1724-0.29980.18530.11310.0309-0.01680.1851-0.01410.10819.120724.994264.1093
153.1117-0.6383-2.62430.92680.6172.22610.07960.70380.1393-0.3403-0.10680.1755-0.0392-1.07750.03840.29680.0256-0.06860.3762-0.00440.27619.309911.36536.9661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 70 )A-2 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 91 )A71 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 125 )A92 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 147 )A126 - 147
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 201 )A148 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 240 )A202 - 240
7X-RAY DIFFRACTION7chain 'A' and (resid 241 through 258 )A241 - 258
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 282 )A259 - 282
9X-RAY DIFFRACTION9chain 'B' and (resid -2 through 25 )B-2 - 25
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 44 )B26 - 44
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 182 )B45 - 182
12X-RAY DIFFRACTION12chain 'B' and (resid 183 through 201 )B183 - 201
13X-RAY DIFFRACTION13chain 'B' and (resid 202 through 240 )B202 - 240
14X-RAY DIFFRACTION14chain 'B' and (resid 241 through 258 )B241 - 258
15X-RAY DIFFRACTION15chain 'B' and (resid 259 through 282 )B259 - 282

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