PDB Short entry for 2MHD HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-NOV-13 2MHD TITLE NMR STRUCTURE OF THE PROTEIN BACUNI_03114 FROM BACTEROIDES UNIFORMIS TITLE 2 ATCC 8492 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 24-132; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES UNIFORMIS; SOURCE 3 ORGANISM_TAXID: 411479; SOURCE 4 ATCC: 8492; SOURCE 5 GENE: BACUNI_03114; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: SPEEDET KEYWDS LIPOCALIN 4, BETA BARREL, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI- KEYWDS 2 BIOLOGY, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR S.SHNITKIND,S.K.DUTTA,P.SERRANO,M.GERALT,K.WUTHRICH,JOINT CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (JCSG) REVDAT 5 14-JUN-23 2MHD 1 REMARK REVDAT 4 01-FEB-23 2MHD 1 SEQADV REVDAT 3 09-SEP-20 2MHD 1 JRNL REMARK REVDAT 2 04-MAR-15 2MHD 1 JRNL TITLE REVDAT 1 04-DEC-13 2MHD 0 JRNL AUTH S.SHNITKIND,S.K.DUTTA,P.SERRANO,M.GERALT,K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE PROTEIN BACUNI_03114 FROM BACTEROIDES JRNL TITL 2 UNIFORMIS ATCC 8492 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, OPALP REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), LUGINBUHL, GUNTERT, REMARK 3 BILLETER AND WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000103617. 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 : 20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 5 MM SODIUM REMARK 210 AZIDE, 1.2 MM [U-99% 13C; U-99% REMARK 210 15N] PROTEIN, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 4D HACANH APSY; REMARK 210 5D HACACONH APSY; 5D CBCACONH REMARK 210 APSY; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 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 : TOPSPIN 2.1, CARA, J-UNIO, CYANA REMARK 210 3.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 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 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 12 TYR A 39 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 12 TYR A 42 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 TRP A 16 CD1 - NE1 - CE2 ANGL. DEV. = 5.9 DEGREES REMARK 500 13 PHE A 33 CB - CG - CD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 13 PHE A 33 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 13 TYR A 42 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 13 TYR A 69 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 15 VAL A 41 CA - CB - CG1 ANGL. DEV. = 9.2 DEGREES REMARK 500 16 TYR A 79 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 18 TYR A 69 CA - CB - CG ANGL. DEV. = 12.7 DEGREES REMARK 500 18 TYR A 69 CB - CG - CD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 19 TYR A 39 CB - CG - CD1 ANGL. DEV. = -4.4 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 GLU A 3 18.18 47.58 REMARK 500 1 VAL A 7 72.07 -66.16 REMARK 500 1 VAL A 13 3.94 -69.62 REMARK 500 1 GLU A 20 103.31 -175.63 REMARK 500 1 ASP A 36 47.58 -166.97 REMARK 500 1 LYS A 37 -68.60 -141.79 REMARK 500 1 LEU A 47 -31.99 -151.54 REMARK 500 1 LYS A 71 10.05 -65.20 REMARK 500 1 CYS A 75 166.92 45.93 REMARK 500 1 THR A 76 -40.62 -150.06 REMARK 500 1 LYS A 87 22.15 -145.86 REMARK 500 1 ALA A 94 -50.06 70.08 REMARK 500 1 LYS A 103 -159.52 -120.17 REMARK 500 1 LYS A 107 -174.38 66.82 REMARK 500 2 GLU A 3 23.14 -77.23 REMARK 500 2 ASP A 5 53.98 -145.12 REMARK 500 2 VAL A 7 93.40 -69.65 REMARK 500 2 ILE A 9 -72.29 -92.16 REMARK 500 2 LYS A 19 41.40 -95.78 REMARK 500 2 GLU A 20 101.74 -166.60 REMARK 500 2 ASP A 36 25.74 -164.85 REMARK 500 2 SER A 45 85.52 174.31 REMARK 500 2 GLU A 63 -87.89 -142.45 REMARK 500 2 LYS A 64 74.62 -168.36 REMARK 500 2 HIS A 74 49.40 -95.73 REMARK 500 2 CYS A 75 -170.10 45.92 REMARK 500 2 THR A 76 -43.70 -172.27 REMARK 500 2 LYS A 87 -3.91 -144.34 REMARK 500 2 ALA A 94 -30.33 52.92 REMARK 500 2 ASP A 102 43.81 -92.78 REMARK 500 2 LYS A 107 178.06 67.56 REMARK 500 3 ASP A 4 62.35 -156.62 REMARK 500 3 PRO A 10 6.08 -67.86 REMARK 500 3 VAL A 13 1.61 -64.32 REMARK 500 3 LYS A 19 27.67 -75.14 REMARK 500 3 ASP A 25 -85.26 58.21 REMARK 500 3 ASP A 26 48.46 -165.45 REMARK 500 3 ASP A 36 24.01 -166.12 REMARK 500 3 LYS A 37 -64.66 -121.82 REMARK 500 3 SER A 45 85.01 46.15 REMARK 500 3 LEU A 47 -78.42 -108.21 REMARK 500 3 GLU A 63 -48.14 174.69 REMARK 500 3 ASP A 70 -165.29 -100.11 REMARK 500 3 LYS A 87 66.66 -154.90 REMARK 500 3 ALA A 94 -39.14 51.95 REMARK 500 3 ASP A 102 74.00 -104.56 REMARK 500 3 LYS A 103 -158.36 -115.50 REMARK 500 3 LYS A 107 -163.12 57.82 REMARK 500 4 ASP A 5 48.47 -150.21 REMARK 500 4 VAL A 13 -6.40 -59.72 REMARK 500 REMARK 500 THIS ENTRY HAS 291 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 1 ASP A 2 4 145.19 REMARK 500 ALA A 35 ASP A 36 6 145.42 REMARK 500 VAL A 41 TYR A 42 8 149.15 REMARK 500 SER A 101 ASP A 102 10 -148.25 REMARK 500 LYS A 90 TRP A 91 19 -148.87 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 TYR A 39 0.08 SIDE CHAIN REMARK 500 1 TYR A 42 0.12 SIDE CHAIN REMARK 500 1 TYR A 57 0.11 SIDE CHAIN REMARK 500 1 TYR A 79 0.10 SIDE CHAIN REMARK 500 3 PHE A 33 0.08 SIDE CHAIN REMARK 500 3 TYR A 69 0.07 SIDE CHAIN REMARK 500 3 TYR A 79 0.08 SIDE CHAIN REMARK 500 4 ARG A 104 0.08 SIDE CHAIN REMARK 500 6 TYR A 108 0.08 SIDE CHAIN REMARK 500 7 TYR A 31 0.07 SIDE CHAIN REMARK 500 8 ARG A 104 0.08 SIDE CHAIN REMARK 500 10 TYR A 42 0.07 SIDE CHAIN REMARK 500 10 TYR A 57 0.07 SIDE CHAIN REMARK 500 10 ARG A 104 0.09 SIDE CHAIN REMARK 500 11 TYR A 79 0.08 SIDE CHAIN REMARK 500 12 PHE A 33 0.08 SIDE CHAIN REMARK 500 12 TYR A 42 0.09 SIDE CHAIN REMARK 500 12 TYR A 79 0.10 SIDE CHAIN REMARK 500 15 TYR A 42 0.07 SIDE CHAIN REMARK 500 16 TYR A 79 0.09 SIDE CHAIN REMARK 500 17 TYR A 79 0.06 SIDE CHAIN REMARK 500 18 TYR A 69 0.10 SIDE CHAIN REMARK 500 19 TYR A 42 0.07 SIDE CHAIN REMARK 500 19 TYR A 57 0.07 SIDE CHAIN REMARK 500 19 ARG A 104 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19627 RELATED DB: BMRB REMARK 900 RELATED ID: JCSG-417984 RELATED DB: TARGETTRACK DBREF 2MHD A 2 110 UNP A7V6A1 A7V6A1_BACUN 24 132 SEQADV 2MHD GLY A 1 UNP A7V6A1 EXPRESSION TAG SEQRES 1 A 110 GLY ASP GLU ASP ASP LYS VAL GLU ILE PRO GLN LEU VAL SEQRES 2 A 110 GLY LYS TRP ILE VAL LYS GLU PRO VAL LEU GLN ASP ASP SEQRES 3 A 110 PHE VAL THR CYS TYR THR PHE ASN ALA ASP LYS THR TYR SEQRES 4 A 110 GLU VAL TYR THR GLY SER PRO LEU SER ASN GLY VAL PRO SEQRES 5 A 110 PHE ARG GLY THR TYR ILE ILE SER LEU ASP GLU LYS LEU SEQRES 6 A 110 ILE LYS LEU TYR ASP LYS GLU GLU HIS CYS THR GLU GLN SEQRES 7 A 110 TYR HIS ILE LEU LYS LEU THR SER LYS GLU MET LYS TRP SEQRES 8 A 110 GLU ASN ALA SER PRO LYS ASP GLY ASN SER ASP LYS ARG SEQRES 9 A 110 LEU GLU LYS TYR ASN ASP HELIX 1 1 ILE A 9 VAL A 13 5 5 SHEET 1 A 7 LYS A 15 ILE A 17 0 SHEET 2 A 7 CYS A 30 PHE A 33 -1 O TYR A 31 N TRP A 16 SHEET 3 A 7 TYR A 39 VAL A 41 -1 O GLU A 40 N THR A 32 SHEET 4 A 7 PHE A 53 SER A 60 -1 O PHE A 53 N VAL A 41 SHEET 5 A 7 LEU A 65 TYR A 69 -1 O TYR A 69 N THR A 56 SHEET 6 A 7 GLU A 77 LEU A 84 -1 O TYR A 79 N ILE A 66 SHEET 7 A 7 MET A 89 GLU A 92 -1 O GLU A 92 N HIS A 80 CISPEP 1 GLU A 20 PRO A 21 1 -17.31 CISPEP 2 GLU A 20 PRO A 21 2 -16.33 CISPEP 3 GLU A 20 PRO A 21 3 -7.01 CISPEP 4 GLU A 20 PRO A 21 4 -4.51 CISPEP 5 GLU A 20 PRO A 21 5 -19.25 CISPEP 6 GLU A 20 PRO A 21 6 -16.40 CISPEP 7 GLU A 20 PRO A 21 7 -14.91 CISPEP 8 GLU A 20 PRO A 21 8 -10.02 CISPEP 9 GLU A 20 PRO A 21 9 -17.91 CISPEP 10 GLU A 20 PRO A 21 10 -19.18 CISPEP 11 GLU A 20 PRO A 21 11 -16.21 CISPEP 12 GLU A 20 PRO A 21 12 -3.29 CISPEP 13 GLU A 20 PRO A 21 13 0.26 CISPEP 14 GLU A 20 PRO A 21 14 -18.11 CISPEP 15 GLU A 20 PRO A 21 15 -16.03 CISPEP 16 GLU A 20 PRO A 21 16 2.07 CISPEP 17 GLU A 20 PRO A 21 17 -6.96 CISPEP 18 GLU A 20 PRO A 21 18 -19.38 CISPEP 19 GLU A 20 PRO A 21 19 -22.55 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