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- PDB-2htd: CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE... -

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Basic information

Entry
Database: PDB / ID: 2htd
TitleCRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION
ComponentsPredicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyPyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Pyridoxamine 5'-phosphate oxidase N-terminal domain-containing protein
Function and homology information
Biological speciesLactobacillus delbrueckii subsp. bulgaricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase (ZP_00387536.1) from Lactobacillus delbrueckii ...Title: Crystal structure of Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase (ZP_00387536.1) from Lactobacillus delbrueckii bulgaricus ATCC BAA-365 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. A suitable ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. A suitable database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase
B: Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2129
Polymers31,6012
Non-polymers6127
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-117 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.104, 71.123, 47.031
Angle α, β, γ (deg.)90.000, 90.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSETHRTHR4AA1 - 2620 - 45
21MSEMSETHRTHR4BB1 - 2620 - 45
32VALVALASNASN5AA27 - 3246 - 51
42VALVALASNASN5BB27 - 3246 - 51
53PROPROALAALA4AA33 - 7452 - 93
63PROPROALAALA4BB33 - 7452 - 93
74ASPASPTHRTHR5AA75 - 8094 - 99
84ASPASPTHRTHR5BB75 - 8094 - 99
95LEULEUALAALA4AA85 - 121104 - 140
105LEULEUALAALA4BB85 - 121104 - 140

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Components

#1: Protein Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase


Mass: 15800.331 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus (bacteria)
Species: Lactobacillus delbrueckii / Strain: ATCC BAA-365 / Gene: ZP_00387536.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GBW8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.39 %
Crystal growTemperature: 277 K / pH: 4
Details: 2.4M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97929,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 2, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
30.979111
ReflectionResolution: 1.595→39.253 Å / Num. obs: 29681 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.683.60.9870.71477440590.98799.8
1.68-1.785.10.6471.12111441460.647100
1.78-1.915.50.3771.92139438660.377100
1.91-2.065.50.2272.72002836120.227100
2.06-2.265.50.154.11849433450.15100
2.26-2.525.50.125.71657030020.12100
2.52-2.915.50.0966.81472426750.096100
2.91-3.575.40.0777.81218922600.077100
3.57-5.045.40.0639.9931817360.06399.4
5.04-47.045.40.05910.852919800.05999

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→39.253 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.448 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.093
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). SULFATE IONS ARE PRESENT IN THE CRYSTALLIZATION SOLUTION. (4) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1486 5 %RANDOM
Rwork0.158 ---
obs0.16 29659 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.14 Å2
2--2.28 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 31 205 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221984
X-RAY DIFFRACTIONr_bond_other_d0.0010.021263
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9792715
X-RAY DIFFRACTIONr_angle_other_deg0.87333134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09726.02388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38915335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.413156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_nbd_refined0.2160.2359
X-RAY DIFFRACTIONr_nbd_other0.1880.21309
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2982
X-RAY DIFFRACTIONr_nbtor_other0.0870.21078
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.220
X-RAY DIFFRACTIONr_mcbond_it1.95431288
X-RAY DIFFRACTIONr_mcbond_other0.7923499
X-RAY DIFFRACTIONr_mcangle_it2.78852033
X-RAY DIFFRACTIONr_scbond_it4.9728777
X-RAY DIFFRACTIONr_scangle_it6.4911673
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1331MEDIUM POSITIONAL0.350.5
57LOOSE POSITIONAL1.055
1331MEDIUM THERMAL1.62
57LOOSE THERMAL3.1310
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 108 -
Rwork0.258 2068 -
obs-2176 98.68 %
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)
13.33360.90411.50533.3060.06262.370.0030.1084-0.1452-0.0642-0.0808-0.23130.14060.26660.07780.10570.01140.01620.04730.00580.128533.501210.672540.3016
21.25830.1719-0.0611.149-0.46941.7617-0.00840.0040.0630.16050.02080.0542-0.1461-0.097-0.01240.0640.0024-0.01240.0208-0.00340.089125.27823.564943.2999
35.4415-0.83790.59961.2366-0.05881.4155-0.0491-0.01630.00360.00880.00910.006-0.0731-0.08640.040.0755-0.01270.0025-0.00010.00050.096726.833423.863439.0704
42.5769-0.4023-0.90953.1161.88824.1353-0.0426-0.2306-0.03910.3506-0.08130.13980.164-0.38230.12390.05210.0035-0.00780.04750.00740.053620.30219.365448.1396
53.11140.19450.05384.17650.00443.4908-0.0813-0.01360.15170.00920.08030.1858-0.1824-0.2650.0010.11190.0264-0.00240.0178-0.01010.113932.093242.129738.4851
61.70280.0255-0.66391.2741-0.40582.5877-0.03140.2235-0.0727-0.15560.0307-0.074-0.00480.02370.00070.0413-0.0026-0.01130.0128-0.0050.038534.358829.485229.396
72.6928-0.0972-0.4370.8069-0.43881.7345-0.03520.30170.0208-0.051-0.0503-0.01120.0386-0.15870.08550.1226-0.0084-0.02390.00990.01690.114936.121735.268327.5009
83.8546-1.481-1.72051.29160.56613.5524-0.01210.33040.0513-0.0482-0.08350.009-0.02540.11270.09550.0591-0.023-0.01680.05750.01750.056740.670834.396123.999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1919 - 38
22AA20 - 5639 - 75
33AA57 - 8276 - 101
44AA83 - 121102 - 140
55BB-2 - 1817 - 37
66BB19 - 7638 - 95
77BB77 - 9796 - 116
88BB98 - 121117 - 140

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