Header list of 2agm.pdb file
Complete list - g 9 2 Bytes
HEADER ISOMERASE 27-JUL-05 2AGM
TITLE SOLUTION STRUCTURE OF THE R-MODULE FROM ALGE4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: POLY(BETA-D-MANNURONATE) C5 EPIMERASE 4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: R-MODULE;
COMPND 5 SYNONYM: MANNURONAN EPIMERASE 4, R-MODULE;
COMPND 6 EC: 5.1.3.-;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII;
SOURCE 3 ORGANISM_TAXID: 354;
SOURCE 4 GENE: R-MODULE SUBUNIT FROM ALGE4;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ER 2566;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFA2 DERIVATIVE OF PTYB11 (NEB)
KEYWDS PARALLEL BETA-ROLL, ISOMERASE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR F.L.AACHMANN,B.I.SVANEM,P.GUNTERT,S.B.PETERSEN,S.VALLA,R.WIMMER
REVDAT 6 14-JUN-23 2AGM 1 REMARK
REVDAT 5 26-FEB-20 2AGM 1 REMARK
REVDAT 4 24-FEB-09 2AGM 1 VERSN
REVDAT 3 04-APR-06 2AGM 1 JRNL
REVDAT 2 24-JAN-06 2AGM 1 JRNL
REVDAT 1 10-JAN-06 2AGM 0
JRNL AUTH F.L.AACHMANN,B.I.SVANEM,P.GUNTERT,S.B.PETERSEN,S.VALLA,
JRNL AUTH 2 R.WIMMER
JRNL TITL NMR STRUCTURE OF THE R-MODULE: A PARALLEL BETA-ROLL SUBUNIT
JRNL TITL 2 FROM AN AZOTOBACTER VINELANDII MANNURONAN C-5 EPIMERASE.
JRNL REF J.BIOL.CHEM. V. 281 7350 2006
JRNL REFN ISSN 0021-9258
JRNL PMID 16407237
JRNL DOI 10.1074/JBC.M510069200
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 2.1.5, OPALP 1.4
REMARK 3 AUTHORS : GUENTERT (CYANA), KORADI, R., BILLETER, M.,
REMARK 3 GUNTERT, P. (OPALP)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1714 UNIQUE RESTRAINTS,
REMARK 3 1576 ARE NOE-DERIVED
REMARK 3 DISTANCE CONSTRAINTS, 138 DIHEDRAL ANGLE RESTRAINTS.
REMARK 4
REMARK 4 2AGM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUL-05.
REMARK 100 THE DEPOSITION ID IS D_1000033869.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.9
REMARK 210 IONIC STRENGTH : 0.17
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.6MM R-MODULE U-99% 13C; U-99%
REMARK 210 15N, 50MM CACL2, 20MM NA-
REMARK 210 HEPES(PH 6.9)
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2.6, XEASY 1.1.13, TALOS
REMARK 210 98.040.21.02, OPALP 1.4
REMARK 210 METHOD USED : DISTANCE GEOMETRY, TORSION ANGLE
REMARK 210 DYNAMICS, ENERGY-MINIMISATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
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: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY AND TORSION ANGLES ESTIMATES FROM SECONDARY
REMARK 210 CHEMICAL SHIFTS USING TALOS
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 3 ASP A 31 N - CA - CB ANGL. DEV. = -10.9 DEGREES
REMARK 500 4 ASP A 11 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 11 ARG A 40 CB - CG - CD ANGL. DEV. = 15.7 DEGREES
REMARK 500 11 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 14 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500 15 ARG A 62 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES
REMARK 500 15 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 19 SER A 60 C - N - CA ANGL. DEV. = 16.8 DEGREES
REMARK 500 20 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.0 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 ASP A 14 -163.08 -175.72
REMARK 500 1 ALA A 49 68.77 -107.41
REMARK 500 1 ALA A 56 42.63 39.29
REMARK 500 1 SER A 60 -74.11 -146.34
REMARK 500 1 ASP A 74 46.38 31.94
REMARK 500 1 GLU A 79 -50.37 -127.61
REMARK 500 1 ASP A 94 10.53 -140.13
REMARK 500 1 TYR A 96 -129.65 -92.05
REMARK 500 1 PHE A 116 94.90 52.00
REMARK 500 1 ALA A 118 -147.47 -134.78
REMARK 500 1 ARG A 123 138.44 178.11
REMARK 500 1 ASP A 132 -52.79 -142.46
REMARK 500 1 HIS A 133 -112.04 -92.27
REMARK 500 1 THR A 150 48.77 -143.84
REMARK 500 1 THR A 151 34.48 -81.21
REMARK 500 1 ASP A 158 -167.92 -102.32
REMARK 500 1 THR A 161 22.43 -79.14
REMARK 500 2 SER A 2 -81.31 -152.96
REMARK 500 2 ASP A 11 -16.04 -147.64
REMARK 500 2 ALA A 29 84.63 -170.85
REMARK 500 2 SER A 55 -2.14 -150.42
REMARK 500 2 ALA A 66 112.89 -167.67
REMARK 500 2 GLU A 79 -52.61 -134.54
REMARK 500 2 TYR A 96 -155.72 -89.75
REMARK 500 2 ASN A 105 -179.72 -66.71
REMARK 500 2 PHE A 116 85.25 25.16
REMARK 500 2 ALA A 118 -142.36 -122.83
REMARK 500 2 ARG A 123 135.50 160.15
REMARK 500 2 HIS A 133 -9.89 64.30
REMARK 500 2 SER A 138 -70.83 -157.24
REMARK 500 2 ALA A 139 -33.26 -141.49
REMARK 500 2 GLU A 152 -157.00 -92.24
REMARK 500 2 LEU A 153 40.73 -73.25
REMARK 500 2 GLU A 154 72.71 25.83
REMARK 500 3 ASP A 13 123.08 -31.32
REMARK 500 3 ASP A 31 48.57 -79.80
REMARK 500 3 ALA A 38 107.86 -59.15
REMARK 500 3 ALA A 49 73.09 -150.25
REMARK 500 3 SER A 55 4.92 -160.75
REMARK 500 3 ASP A 59 90.95 -69.77
REMARK 500 3 SER A 60 -34.82 -171.22
REMARK 500 3 ASP A 64 -68.09 -28.88
REMARK 500 3 ASP A 74 63.85 39.16
REMARK 500 3 GLU A 79 -36.79 -130.41
REMARK 500 3 ASN A 105 -175.65 -69.44
REMARK 500 3 PHE A 116 67.57 36.95
REMARK 500 3 ALA A 118 -145.57 -126.51
REMARK 500 3 ARG A 123 128.65 -170.07
REMARK 500 3 ASP A 132 13.52 -140.51
REMARK 500 3 THR A 134 74.08 43.48
REMARK 500
REMARK 500 THIS ENTRY HAS 354 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 40 0.11 SIDE CHAIN
REMARK 500 2 ARG A 42 0.09 SIDE CHAIN
REMARK 500 2 ARG A 62 0.09 SIDE CHAIN
REMARK 500 3 ARG A 62 0.17 SIDE CHAIN
REMARK 500 4 ARG A 40 0.10 SIDE CHAIN
REMARK 500 5 TYR A 61 0.07 SIDE CHAIN
REMARK 500 5 ARG A 62 0.12 SIDE CHAIN
REMARK 500 6 ARG A 24 0.12 SIDE CHAIN
REMARK 500 6 ARG A 40 0.09 SIDE CHAIN
REMARK 500 6 TYR A 112 0.11 SIDE CHAIN
REMARK 500 7 ARG A 124 0.12 SIDE CHAIN
REMARK 500 7 PHE A 125 0.08 SIDE CHAIN
REMARK 500 8 ARG A 40 0.09 SIDE CHAIN
REMARK 500 12 ARG A 81 0.08 SIDE CHAIN
REMARK 500 12 ARG A 124 0.09 SIDE CHAIN
REMARK 500 13 ARG A 62 0.16 SIDE CHAIN
REMARK 500 14 ARG A 123 0.10 SIDE CHAIN
REMARK 500 16 ARG A 24 0.11 SIDE CHAIN
REMARK 500 17 ARG A 124 0.09 SIDE CHAIN
REMARK 500 20 ARG A 57 0.15 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 8 GLY A 21 10.53
REMARK 500 15 GLY A 21 12.34
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6390 RELATED DB: BMRB
DBREF 2AGM A 1 167 UNP Q44493 ALGE4_AZOVI 387 553
SEQRES 1 A 167 GLY SER ASP GLY GLU PRO LEU VAL GLY GLY ASP THR ASP
SEQRES 2 A 167 ASP GLN LEU GLN GLY GLY SER GLY ALA ASP ARG LEU ASP
SEQRES 3 A 167 GLY GLY ALA GLY ASP ASP ILE LEU ASP GLY GLY ALA GLY
SEQRES 4 A 167 ARG ASP ARG LEU SER GLY GLY ALA GLY ALA ASP THR PHE
SEQRES 5 A 167 VAL PHE SER ALA ARG GLU ASP SER TYR ARG THR ASP THR
SEQRES 6 A 167 ALA VAL PHE ASN ASP LEU ILE LEU ASP PHE GLU ALA SER
SEQRES 7 A 167 GLU ASP ARG ILE ASP LEU SER ALA LEU GLY PHE SER GLY
SEQRES 8 A 167 LEU GLY ASP GLY TYR GLY GLY THR LEU LEU LEU LYS THR
SEQRES 9 A 167 ASN ALA GLU GLY THR ARG THR TYR LEU LYS SER PHE GLU
SEQRES 10 A 167 ALA ASP ALA GLU GLY ARG ARG PHE GLU VAL ALA LEU ASP
SEQRES 11 A 167 GLY ASP HIS THR GLY ASP LEU SER ALA ALA ASN VAL VAL
SEQRES 12 A 167 PHE ALA ALA THR GLY THR THR THR GLU LEU GLU VAL LEU
SEQRES 13 A 167 GLY ASP SER GLY THR GLN ALA GLY ALA ILE VAL
SHEET 1 A 7 LEU A 7 GLY A 10 0
SHEET 2 A 7 LEU A 25 GLY A 28 1 O ASP A 26 N LEU A 7
SHEET 3 A 7 ARG A 42 GLY A 46 1 O GLY A 45 N GLY A 28
SHEET 4 A 7 LEU A 71 PHE A 75 1 O LEU A 73 N LEU A 43
SHEET 5 A 7 ALA A 128 GLY A 131 1 O ASP A 130 N ILE A 72
SHEET 6 A 7 ARG A 110 SER A 115 -1 N THR A 111 O LEU A 129
SHEET 7 A 7 LEU A 100 THR A 104 -1 N LYS A 103 O TYR A 112
SHEET 1 B 4 GLN A 15 GLN A 17 0
SHEET 2 B 4 ILE A 33 ASP A 35 1 O ILE A 33 N LEU A 16
SHEET 3 B 4 THR A 51 VAL A 53 1 O VAL A 53 N LEU A 34
SHEET 4 B 4 ARG A 81 ASP A 83 1 O ARG A 81 N PHE A 52
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
Complete list - g 9 2 Bytes