PDB Short entry for 2JMM HEADER MEMBRANE PROTEIN 20-NOV-06 2JMM TITLE NMR SOLUTION STRUCTURE OF A MINIMAL TRANSMEMBRANE BETA-BARREL PLATFORM TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OUTER MEMBRANE PROTEIN II*; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: OMPA, CON, TOLG, TUT; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-3B KEYWDS MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.U.JOHANSSON,S.ALIOTH,K.HU,R.WALSER,R.KOEBNIK,K.PERVUSHIN REVDAT 4 20-DEC-23 2JMM 1 REMARK REVDAT 3 05-FEB-20 2JMM 1 REMARK REVDAT 2 24-FEB-09 2JMM 1 VERSN REVDAT 1 03-JUL-07 2JMM 0 JRNL AUTH M.U.JOHANSSON,S.ALIOTH,K.HU,R.WALSER,R.KOEBNIK,K.PERVUSHIN JRNL TITL A MINIMAL TRANSMEMBRANE BETA-BARREL PLATFORM PROTEIN STUDIED JRNL TITL 2 BY NUCLEAR MAGNETIC RESONANCE JRNL REF BIOCHEMISTRY V. 46 1128 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17260943 JRNL DOI 10.1021/BI061265E REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, GROMACS REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 LINDAHL, HESS AND VAN DER SPOEL (GROMACS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JMM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000100022. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N; REMARK 210 80% 2H] BBP+EF, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : GROMACS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 160 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: 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 ARG A 127 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 TYR A 76 CB - CG - CD2 ANGL. DEV. = -4.0 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 PRO A 2 31.78 -78.51 REMARK 500 1 ASP A 4 99.20 72.21 REMARK 500 1 SER A 19 80.56 -67.18 REMARK 500 1 TYR A 37 -79.00 -175.43 REMARK 500 1 ARG A 49 -70.61 -128.07 REMARK 500 1 PRO A 51 30.54 -70.27 REMARK 500 1 THR A 70 28.41 -67.88 REMARK 500 1 ASP A 71 -68.20 -169.82 REMARK 500 1 ASP A 72 87.48 -170.05 REMARK 500 1 ARG A 85 -36.01 68.24 REMARK 500 1 ALA A 86 -54.06 70.70 REMARK 500 1 ASP A 90 -39.58 -169.84 REMARK 500 1 LYS A 91 88.28 56.61 REMARK 500 1 ILE A 116 95.62 -62.20 REMARK 500 1 ARG A 118 -143.37 -175.38 REMARK 500 1 ARG A 119 99.85 -62.34 REMARK 500 1 ILE A 120 85.56 64.63 REMARK 500 1 GLU A 123 -83.84 -138.74 REMARK 500 1 ASN A 134 -162.84 54.41 REMARK 500 1 ALA A 136 -171.89 54.64 REMARK 500 1 SER A 137 85.30 -65.99 REMARK 500 1 ASP A 138 -101.63 -102.31 REMARK 500 1 PHE A 150 -77.61 69.55 REMARK 500 1 GLU A 154 85.68 -67.79 REMARK 500 1 ALA A 155 99.14 -66.88 REMARK 500 2 ASP A 4 45.69 -164.58 REMARK 500 2 GLN A 17 99.20 -49.80 REMARK 500 2 TYR A 18 25.91 49.58 REMARK 500 2 ARG A 20 -30.98 72.36 REMARK 500 2 GLU A 21 97.25 -59.54 REMARK 500 2 PRO A 36 84.09 -67.63 REMARK 500 2 TYR A 37 -41.27 158.82 REMARK 500 2 LEU A 47 75.92 -118.87 REMARK 500 2 ARG A 49 -88.54 -57.72 REMARK 500 2 ARG A 52 -62.38 174.21 REMARK 500 2 LYS A 53 -112.39 -111.48 REMARK 500 2 ALA A 54 -142.00 61.25 REMARK 500 2 ASP A 71 79.73 -62.66 REMARK 500 2 ASP A 72 -39.24 -174.14 REMARK 500 2 ASP A 87 90.62 54.61 REMARK 500 2 ASN A 94 -165.32 65.95 REMARK 500 2 ILE A 116 144.04 62.95 REMARK 500 2 ARG A 117 155.38 63.33 REMARK 500 2 ARG A 118 -50.28 69.33 REMARK 500 2 ASN A 135 -58.01 -13.85 REMARK 500 2 ASN A 139 -50.02 -7.15 REMARK 500 2 PHE A 150 139.02 54.72 REMARK 500 3 ASN A 5 48.67 178.89 REMARK 500 3 GLN A 17 -76.91 -14.76 REMARK 500 3 GLU A 21 -70.86 -142.74 REMARK 500 REMARK 500 THIS ENTRY HAS 267 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 THR A 70 ASP A 71 4 148.23 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 18 0.09 SIDE CHAIN REMARK 500 1 TYR A 32 0.10 SIDE CHAIN REMARK 500 1 TYR A 76 0.09 SIDE CHAIN REMARK 500 1 TYR A 130 0.11 SIDE CHAIN REMARK 500 2 TYR A 37 0.06 SIDE CHAIN REMARK 500 2 TYR A 114 0.14 SIDE CHAIN REMARK 500 2 TYR A 148 0.14 SIDE CHAIN REMARK 500 3 TYR A 65 0.08 SIDE CHAIN REMARK 500 4 TYR A 76 0.06 SIDE CHAIN REMARK 500 5 TYR A 18 0.13 SIDE CHAIN REMARK 500 5 TYR A 32 0.07 SIDE CHAIN REMARK 500 5 TYR A 65 0.08 SIDE CHAIN REMARK 500 5 TYR A 76 0.08 SIDE CHAIN REMARK 500 5 TYR A 130 0.09 SIDE CHAIN REMARK 500 6 TYR A 65 0.06 SIDE CHAIN REMARK 500 6 TYR A 76 0.14 SIDE CHAIN REMARK 500 6 TYR A 130 0.08 SIDE CHAIN REMARK 500 7 TYR A 130 0.09 SIDE CHAIN REMARK 500 7 TYR A 148 0.16 SIDE CHAIN REMARK 500 8 TYR A 8 0.10 SIDE CHAIN REMARK 500 8 TYR A 76 0.07 SIDE CHAIN REMARK 500 9 TYR A 8 0.14 SIDE CHAIN REMARK 500 9 TYR A 65 0.14 SIDE CHAIN REMARK 500 9 TYR A 76 0.07 SIDE CHAIN REMARK 500 9 TYR A 114 0.07 SIDE CHAIN REMARK 500 9 TYR A 148 0.18 SIDE CHAIN REMARK 500 10 TYR A 76 0.08 SIDE CHAIN REMARK 500 10 TYR A 114 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 2 ALA A 11 13.34 REMARK 500 2 GLU A 21 10.30 REMARK 500 2 ASP A 71 10.51 REMARK 500 2 GLY A 93 -10.10 REMARK 500 3 GLN A 17 10.04 REMARK 500 3 VAL A 34 10.04 REMARK 500 4 TYR A 130 19.20 REMARK 500 5 ASP A 71 10.48 REMARK 500 5 THR A 77 14.87 REMARK 500 5 ILE A 120 10.88 REMARK 500 6 ALA A 11 14.07 REMARK 500 6 ALA A 86 12.01 REMARK 500 7 ILE A 75 13.10 REMARK 500 8 ALA A 28 10.16 REMARK 500 8 GLN A 33 11.88 REMARK 500 9 GLY A 81 16.30 REMARK 500 10 LEU A 73 -10.58 REMARK 500 10 ILE A 75 16.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15045 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS STATE THAT THE SEQUENCE IS A MODIFICATION REMARK 999 TO THE OMPA_ECOLI UNIPROTKB/SWISS-PROT ENTRY P0A910 REMARK 999 SEQUENCE. RESIDUES 40-52 OF THE FIRST EXTRACELLULAR LOOP REMARK 999 ARE REPLACED BY SR. RESIDUES 84-93 OF THE SECOND REMARK 999 EXTRACELLULAR LOOP ARE REPLACED BY R. RESIDUE I108 IN REMARK 999 PERIPLASMIC LOOP 2 IS REPLACED BY KLG. RESIDUES 127-139 REMARK 999 OF THE THIRD EXTRACELLULAR LOOP ARE SHORTENED TO TS AND REMARK 999 12 AMINO ACIDS CORRESPONDING TO THE THIRD EF-HAND LOOP REMARK 999 (DKDGNGYISAAE) AND AMINO ACIDS AS WERE ADDED FOR REMARK 999 "FLEXIBILITY". RESIDUES 148-155 IN PERIPLASMIC LOOP 3 IS REMARK 999 REPLACED BY THE SEQUENCE EYVIRRRITPE. RESIDUES 168-178 OF REMARK 999 THE FOURTH EXTRACELLULAR LOOP ARE REPLACED BY AS. DBREF 2JMM A 2 156 UNP P0A910 OMPA_ECOLI 43 197 SEQRES 1 A 156 MET PRO LYS ASP ASN THR TRP TYR THR GLY ALA LYS LEU SEQRES 2 A 156 GLY TRP SER GLN TYR SER ARG GLU ASN GLN LEU GLY ALA SEQRES 3 A 156 GLY ALA PHE GLY GLY TYR GLN VAL ASN PRO TYR VAL GLY SEQRES 4 A 156 PHE GLU MET GLY TYR ASP TRP LEU GLY ARG MET PRO ARG SEQRES 5 A 156 LYS ALA GLN GLY VAL GLN LEU THR ALA LYS LEU GLY TYR SEQRES 6 A 156 PRO LYS LEU GLY THR ASP ASP LEU ASP ILE TYR THR ARG SEQRES 7 A 156 LEU GLY GLY MET VAL TRP ARG ALA ASP THR SER ASP LYS SEQRES 8 A 156 ASP GLY ASN GLY TYR ILE SER ALA ALA GLU ALA SER VAL SEQRES 9 A 156 SER PRO VAL PHE ALA GLY GLY VAL GLU TYR VAL ILE ARG SEQRES 10 A 156 ARG ARG ILE THR PRO GLU ILE ALA THR ARG LEU GLU TYR SEQRES 11 A 156 GLN TRP THR ASN ASN ALA SER ASP ASN GLY MET LEU SER SEQRES 12 A 156 LEU GLY VAL SER TYR ARG PHE GLY GLN GLY GLU ALA ALA SHEET 1 A 9 THR A 6 SER A 16 0 SHEET 2 A 9 GLY A 25 GLN A 33 -1 O GLN A 33 N THR A 6 SHEET 3 A 9 VAL A 38 LEU A 47 -1 O TYR A 44 N ALA A 28 SHEET 4 A 9 ALA A 54 TYR A 65 -1 O GLY A 56 N ASP A 45 SHEET 5 A 9 ASP A 74 TRP A 84 -1 O VAL A 83 N VAL A 57 SHEET 6 A 9 PRO A 106 VAL A 115 -1 O GLY A 111 N TYR A 76 SHEET 7 A 9 ILE A 124 THR A 133 -1 O TRP A 132 N PHE A 108 SHEET 8 A 9 ASN A 139 ARG A 149 -1 O SER A 143 N GLU A 129 SHEET 9 A 9 THR A 6 SER A 16 -1 N LEU A 13 O LEU A 144 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