HEADER FLAVOPROTEIN 13-NOV-14 2MWM
TITLE NMR STRUCTURE OF THE PROTEIN YP_193882.1 FROM LACTOBACILLUS
TITLE 2 ACIDOPHILUS NCFM IN PRESENCE OF FMN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PUTATIVE TRP REPRESSOR BINDING PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS ACIDOPHILUS;
SOURCE 3 ORGANISM_TAXID: 272621;
SOURCE 4 STRAIN: ATCC 700396 / NCK56 / N2 / NCFM;
SOURCE 5 GENE: LBA1001;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET
KEYWDS HUMAN GUT MICROBIOME SECRETED PROTEIN, FLAVODOXIN 4, FLAVOPROTEIN,
KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, JOINT
KEYWDS 3 CENTER FOR STRUCTURAL GENOMICS, JCSG
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR S.K.DUTTA,P.SERRANO,M.GERALT,K.WUTHRICH,JOINT CENTER FOR STRUCTURAL
AUTHOR 2 GENOMICS (JCSG)
REVDAT 2 14-JUN-23 2MWM 1 REMARK SEQADV
REVDAT 1 10-DEC-14 2MWM 0
JRNL AUTH S.K.DUTTA,P.SERRANO,M.GERALT,K.WUTHRICH
JRNL TITL NMR STRUCTURE OF THE PROTEIN YP_193882.1 FROM LACTOBACILLUS
JRNL TITL 2 ACIDOPHILUS NCFM IN PRESENCE OF FMN
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 3.0
REMARK 3 AUTHORS : HERRMANN, GUNTERT AND WUTHRICH
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2MWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-14.
REMARK 100 THE DEPOSITION ID IS D_1000104135.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : 0.0798
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-99% 13C; U-98% 15N]
REMARK 210 PROTEIN, 20 MM SODIUM PHOSPHATE,
REMARK 210 50 MM SODIUM CHLORIDE, 5 MM
REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : APSY 4D-HACANH; APSY 5D
REMARK 210 -HACACONH; APSY 5D-CBCACONH; 2D
REMARK 210 1H-15N HSQC; 3D 1H-15N NOESY; 3D
REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H-
REMARK 210 13C NOESY AROMATIC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CYANA 3.0, TOPSPIN 3.1, PROSA,
REMARK 210 OPAL, CARA
REMARK 210 METHOD USED : MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 80
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O PRO A 65 HG1 THR A 97 1.60
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 5 MET A 20 CG - SD - CE ANGL. DEV. = -10.0 DEGREES
REMARK 500 5 TYR A 123 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 6 TYR A 10 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 7 ASP A 56 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES
REMARK 500 7 PHE A 113 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 9 TYR A 10 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 9 VAL A 86 CG1 - CB - CG2 ANGL. DEV. = 10.0 DEGREES
REMARK 500 9 VAL A 86 CA - CB - CG2 ANGL. DEV. = 12.0 DEGREES
REMARK 500 10 ASP A 56 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES
REMARK 500 11 TYR A 123 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 12 ARG A 141 CD - NE - CZ ANGL. DEV. = 9.8 DEGREES
REMARK 500 13 VAL A 86 CA - CB - CG2 ANGL. DEV. = 12.7 DEGREES
REMARK 500 14 TYR A 10 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 15 VAL A 86 CG1 - CB - CG2 ANGL. DEV. = -9.7 DEGREES
REMARK 500 15 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 20 TYR A 10 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ALA A 3 80.24 -159.11
REMARK 500 1 TRP A 13 -85.07 -57.71
REMARK 500 1 SER A 14 65.68 -162.62
REMARK 500 1 LYS A 23 -74.42 -57.03
REMARK 500 1 LYS A 29 177.30 -54.57
REMARK 500 1 ASP A 30 69.65 -54.65
REMARK 500 1 ASP A 44 -161.51 -119.35
REMARK 500 1 ILE A 58 -59.57 -123.54
REMARK 500 1 PRO A 91 -178.00 -65.76
REMARK 500 1 ALA A 116 48.01 -90.66
REMARK 500 1 ALA A 131 21.24 -159.64
REMARK 500 1 ASP A 142 -161.55 52.81
REMARK 500 2 MET A 2 77.56 -151.15
REMARK 500 2 ALA A 3 88.39 -160.74
REMARK 500 2 TRP A 13 -78.88 -62.56
REMARK 500 2 GLU A 16 -78.67 -75.28
REMARK 500 2 ASP A 30 27.70 49.76
REMARK 500 2 VAL A 38 -169.06 -109.97
REMARK 500 2 TRP A 87 -169.34 -111.33
REMARK 500 2 SER A 88 81.86 -45.72
REMARK 500 2 ALA A 92 29.63 -74.52
REMARK 500 2 PHE A 113 -177.93 -170.78
REMARK 500 2 ASN A 119 13.27 53.96
REMARK 500 2 ALA A 131 42.16 -155.16
REMARK 500 2 ASP A 142 -179.85 -178.43
REMARK 500 2 SER A 150 36.94 -150.67
REMARK 500 3 LYS A 4 91.39 -162.31
REMARK 500 3 LYS A 29 -164.70 -53.32
REMARK 500 3 ASP A 30 47.65 -70.29
REMARK 500 3 TYR A 48 -35.78 -133.68
REMARK 500 3 ASP A 63 -179.03 -68.49
REMARK 500 3 ASN A 75 -49.05 -159.72
REMARK 500 3 SER A 88 15.45 -63.76
REMARK 500 3 ALA A 92 34.54 -74.85
REMARK 500 3 ASP A 142 -179.27 54.11
REMARK 500 3 GLU A 145 10.43 -141.13
REMARK 500 4 MET A 2 -75.46 -69.56
REMARK 500 4 ALA A 3 49.90 -149.01
REMARK 500 4 TRP A 13 -85.16 -138.71
REMARK 500 4 GLU A 16 -78.08 -88.63
REMARK 500 4 LYS A 29 -172.73 -58.63
REMARK 500 4 ASP A 30 26.70 -61.96
REMARK 500 4 ALA A 45 2.29 50.55
REMARK 500 4 ASN A 76 36.81 -87.18
REMARK 500 4 SER A 88 91.52 -47.72
REMARK 500 4 ALA A 131 -8.06 -143.09
REMARK 500 4 ASP A 142 -154.05 54.55
REMARK 500 4 SER A 150 18.95 -151.86
REMARK 500 5 ALA A 3 69.57 -155.07
REMARK 500 5 LYS A 4 19.57 -141.12
REMARK 500
REMARK 500 THIS ENTRY HAS 292 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 ARG A 141 0.09 SIDE CHAIN
REMARK 500 2 TYR A 10 0.07 SIDE CHAIN
REMARK 500 2 ARG A 106 0.09 SIDE CHAIN
REMARK 500 2 TYR A 123 0.07 SIDE CHAIN
REMARK 500 3 TYR A 90 0.07 SIDE CHAIN
REMARK 500 4 TYR A 10 0.08 SIDE CHAIN
REMARK 500 4 TYR A 77 0.12 SIDE CHAIN
REMARK 500 4 TYR A 90 0.10 SIDE CHAIN
REMARK 500 5 TYR A 10 0.12 SIDE CHAIN
REMARK 500 5 TYR A 48 0.12 SIDE CHAIN
REMARK 500 5 TYR A 105 0.10 SIDE CHAIN
REMARK 500 5 TYR A 123 0.12 SIDE CHAIN
REMARK 500 6 TYR A 77 0.06 SIDE CHAIN
REMARK 500 7 TYR A 10 0.10 SIDE CHAIN
REMARK 500 7 TYR A 90 0.07 SIDE CHAIN
REMARK 500 8 TYR A 48 0.10 SIDE CHAIN
REMARK 500 9 TYR A 10 0.13 SIDE CHAIN
REMARK 500 9 TYR A 77 0.09 SIDE CHAIN
REMARK 500 9 TYR A 123 0.07 SIDE CHAIN
REMARK 500 10 TYR A 10 0.07 SIDE CHAIN
REMARK 500 11 TYR A 48 0.15 SIDE CHAIN
REMARK 500 11 ARG A 106 0.09 SIDE CHAIN
REMARK 500 11 TYR A 123 0.07 SIDE CHAIN
REMARK 500 13 TYR A 10 0.07 SIDE CHAIN
REMARK 500 13 TYR A 74 0.07 SIDE CHAIN
REMARK 500 14 TYR A 90 0.12 SIDE CHAIN
REMARK 500 15 TYR A 10 0.11 SIDE CHAIN
REMARK 500 15 TYR A 48 0.15 SIDE CHAIN
REMARK 500 15 TYR A 77 0.10 SIDE CHAIN
REMARK 500 16 TYR A 123 0.11 SIDE CHAIN
REMARK 500 17 TYR A 74 0.07 SIDE CHAIN
REMARK 500 17 TYR A 77 0.07 SIDE CHAIN
REMARK 500 17 ARG A 141 0.09 SIDE CHAIN
REMARK 500 18 TYR A 10 0.07 SIDE CHAIN
REMARK 500 18 TYR A 90 0.08 SIDE CHAIN
REMARK 500 19 TYR A 48 0.14 SIDE CHAIN
REMARK 500 19 TYR A 123 0.07 SIDE CHAIN
REMARK 500 20 TYR A 10 0.08 SIDE CHAIN
REMARK 500 20 TYR A 77 0.08 SIDE CHAIN
REMARK 500 20 PHE A 113 0.19 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3EDO RELATED DB: PDB
REMARK 900 RELATED ID: 25342 RELATED DB: BMRB
REMARK 900 RELATED ID: JCSG-388454 RELATED DB: TARGETTRACK
DBREF 2MWM A 2 151 UNP Q5FKC3 Q5FKC3_LACAC 1 150
SEQADV 2MWM GLY A 1 UNP Q5FKC3 EXPRESSION TAG
SEQRES 1 A 151 GLY MET ALA LYS LYS THR LEU ILE LEU TYR TYR SER TRP
SEQRES 2 A 151 SER GLY GLU THR LYS LYS MET ALA GLU LYS ILE ASN SER
SEQRES 3 A 151 GLU ILE LYS ASP SER GLU LEU LYS GLU VAL LYS VAL SER
SEQRES 4 A 151 GLU GLY THR PHE ASP ALA ASP MET TYR LYS THR SER ASP
SEQRES 5 A 151 ILE ALA LEU ASP GLN ILE GLN GLY ASN LYS ASP PHE PRO
SEQRES 6 A 151 GLU ILE GLN LEU ASP ASN ILE ASP TYR ASN ASN TYR ASP
SEQRES 7 A 151 LEU ILE LEU ILE GLY SER PRO VAL TRP SER GLY TYR PRO
SEQRES 8 A 151 ALA THR PRO ILE LYS THR LEU LEU ASP GLN MET LYS ASN
SEQRES 9 A 151 TYR ARG GLY GLU VAL ALA SER PHE PHE THR SER ALA GLY
SEQRES 10 A 151 THR ASN HIS LYS ALA TYR VAL SER HIS PHE ASN GLU TRP
SEQRES 11 A 151 ALA ASP GLY LEU ASN VAL ILE GLY VAL ALA ARG ASP ASP
SEQRES 12 A 151 SER GLU VAL ASP LYS TRP SER LYS
HELIX 1 1 GLU A 16 ASN A 25 1 10
HELIX 2 2 MET A 47 GLN A 57 1 11
HELIX 3 3 ASP A 73 TYR A 77 5 5
HELIX 4 4 THR A 93 LYS A 103 1 11
HELIX 5 5 LYS A 121 TRP A 130 1 10
HELIX 6 6 GLU A 145 SER A 150 1 6
SHEET 1 A 4 GLU A 32 GLU A 35 0
SHEET 2 A 4 THR A 6 TYR A 10 1 N ILE A 8 O LYS A 34
SHEET 3 A 4 LEU A 79 SER A 84 1 O LEU A 81 N LEU A 7
SHEET 4 A 4 GLU A 108 PHE A 113 1 O PHE A 112 N ILE A 82
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END
