HEADER OXIDOREDUCTASE 01-MAY-18 6DAM TITLE CRYSTAL STRUCTURE OF LANTHANIDE-DEPENDENT METHANOL DEHYDROGENASE XOXF TITLE 2 FROM METHYLOMICROBIUM BURYATENSE 5G COMPND MOL_ID: 1; COMPND 2 MOLECULE: LANTHANIDE-DEPENDENT METHANOL DEHYDROGENASE XOXF; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOMICROBIUM BURYATENSE 5G; SOURCE 3 ORGANISM_TAXID: 675511 KEYWDS DEHYDROGENASE, PQQ, METHANOL, XOXF, LANTHANIDE, LANTHANUM, KEYWDS 2 METHANOTROPH, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.DENG,S.Y.RO,A.C.ROSENZWEIG REVDAT 4 04-OCT-23 6DAM 1 REMARK REVDAT 3 18-DEC-19 6DAM 1 REMARK REVDAT 2 07-NOV-18 6DAM 1 JRNL REVDAT 1 05-SEP-18 6DAM 0 JRNL AUTH Y.W.DENG,S.Y.RO,A.C.ROSENZWEIG JRNL TITL STRUCTURE AND FUNCTION OF THE LANTHANIDE-DEPENDENT METHANOL JRNL TITL 2 DEHYDROGENASE XOXF FROM THE METHANOTROPH METHYLOMICROBIUM JRNL TITL 3 BURYATENSE 5GB1C. JRNL REF J. BIOL. INORG. CHEM. V. 23 1037 2018 JRNL REFN ESSN 1432-1327 JRNL PMID 30132076 JRNL DOI 10.1007/S00775-018-1604-2 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 39621 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2013 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.6766 - 4.4532 1.00 3047 162 0.1314 0.1606 REMARK 3 2 4.4532 - 3.5370 1.00 2923 167 0.1210 0.1360 REMARK 3 3 3.5370 - 3.0905 1.00 2895 151 0.1426 0.1750 REMARK 3 4 3.0905 - 2.8083 1.00 2873 156 0.1560 0.1647 REMARK 3 5 2.8083 - 2.6071 0.99 2860 155 0.1616 0.2052 REMARK 3 6 2.6071 - 2.4535 0.97 2749 174 0.1615 0.1870 REMARK 3 7 2.4535 - 2.3307 0.95 2693 153 0.1593 0.2137 REMARK 3 8 2.3307 - 2.2293 0.94 2689 116 0.1576 0.2108 REMARK 3 9 2.2293 - 2.1435 0.93 2641 145 0.1701 0.2223 REMARK 3 10 2.1435 - 2.0696 0.92 2609 148 0.1739 0.1997 REMARK 3 11 2.0696 - 2.0049 0.89 2533 123 0.1757 0.2373 REMARK 3 12 2.0049 - 1.9476 0.86 2443 132 0.1826 0.1916 REMARK 3 13 1.9476 - 1.8963 0.83 2345 136 0.1987 0.2517 REMARK 3 14 1.8963 - 1.8501 0.81 2308 95 0.2297 0.2695 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 4526 REMARK 3 ANGLE : 0.891 6175 REMARK 3 CHIRALITY : 0.058 649 REMARK 3 PLANARITY : 0.005 795 REMARK 3 DIHEDRAL : 4.570 2578 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 413 THROUGH 515 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4542 112.9484 21.8475 REMARK 3 T TENSOR REMARK 3 T11: 0.1412 T22: 0.1745 REMARK 3 T33: 0.1461 T12: 0.0215 REMARK 3 T13: -0.0081 T23: -0.0143 REMARK 3 L TENSOR REMARK 3 L11: 0.4906 L22: 0.5356 REMARK 3 L33: 0.6853 L12: 0.0131 REMARK 3 L13: -0.1177 L23: 0.1013 REMARK 3 S TENSOR REMARK 3 S11: 0.0309 S12: 0.0257 S13: 0.0567 REMARK 3 S21: -0.0412 S22: -0.0112 S23: 0.0634 REMARK 3 S31: -0.0195 S32: -0.1238 S33: -0.0032 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 516 THROUGH 617 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5022 104.3663 37.3703 REMARK 3 T TENSOR REMARK 3 T11: 0.1459 T22: 0.1476 REMARK 3 T33: 0.1253 T12: -0.0000 REMARK 3 T13: -0.0244 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.8390 L22: 0.8788 REMARK 3 L33: 1.2093 L12: 0.2414 REMARK 3 L13: -0.2377 L23: 0.2856 REMARK 3 S TENSOR REMARK 3 S11: 0.0363 S12: -0.0569 S13: -0.0306 REMARK 3 S21: -0.0320 S22: -0.0036 S23: 0.0247 REMARK 3 S31: 0.1060 S32: -0.1623 S33: -0.0196 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 168 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.8748 114.1168 35.6807 REMARK 3 T TENSOR REMARK 3 T11: 0.1197 T22: 0.1395 REMARK 3 T33: 0.1336 T12: 0.0216 REMARK 3 T13: -0.0134 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.5591 L22: 0.6394 REMARK 3 L33: 1.1352 L12: 0.3529 REMARK 3 L13: 0.0705 L23: 0.0049 REMARK 3 S TENSOR REMARK 3 S11: 0.0278 S12: -0.0028 S13: -0.0103 REMARK 3 S21: 0.0107 S22: -0.0214 S23: -0.0412 REMARK 3 S31: -0.0079 S32: 0.1208 S33: -0.0053 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 169 THROUGH 412 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0784 121.8023 12.2654 REMARK 3 T TENSOR REMARK 3 T11: 0.1484 T22: 0.1602 REMARK 3 T33: 0.1415 T12: 0.0383 REMARK 3 T13: 0.0110 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.6504 L22: 0.5923 REMARK 3 L33: 1.0082 L12: 0.2483 REMARK 3 L13: 0.0070 L23: 0.0167 REMARK 3 S TENSOR REMARK 3 S11: 0.0359 S12: 0.0851 S13: 0.0571 REMARK 3 S21: -0.0710 S22: -0.0208 S23: -0.0053 REMARK 3 S31: -0.0807 S32: -0.0012 S33: -0.0099 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-17; 07-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 21-ID-G; 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790; 1.968 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; PIXEL REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD; DECTRIS REMARK 200 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39629 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 51.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4MAE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE, PH 6.5, AND 20% PEG 8000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 95.88600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 95.88600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.67350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.14150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.67350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.14150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 95.88600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.67350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.14150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 95.88600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.67350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.14150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1231 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1272 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1295 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 LYS A 3 REMARK 465 PRO A 4 REMARK 465 VAL A 5 REMARK 465 LYS A 6 REMARK 465 SER A 7 REMARK 465 TRP A 8 REMARK 465 LEU A 9 REMARK 465 ILE A 10 REMARK 465 ALA A 11 REMARK 465 SER A 12 REMARK 465 THR A 13 REMARK 465 VAL A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 LEU A 18 REMARK 465 ALA A 19 REMARK 465 VAL A 20 REMARK 465 PRO A 21 REMARK 465 ALA A 22 REMARK 465 VAL A 23 REMARK 465 SER A 24 REMARK 465 GLN A 25 REMARK 465 ALA A 26 REMARK 465 ALA A 571 REMARK 465 GLY A 572 REMARK 465 ILE A 573 REMARK 465 GLY A 574 REMARK 465 ILE A 575 REMARK 465 ALA A 576 REMARK 465 ALA A 577 REMARK 465 GLY A 578 REMARK 465 LEU A 579 REMARK 465 ASP A 580 REMARK 465 SER A 581 REMARK 465 GLY A 582 REMARK 465 GLU A 583 REMARK 465 GLU A 584 REMARK 465 SER A 585 REMARK 465 SER A 586 REMARK 465 ASN A 587 REMARK 465 SER A 588 REMARK 465 GLU A 589 REMARK 465 GLY A 590 REMARK 465 LEU A 591 REMARK 465 GLY A 592 REMARK 465 ALA A 593 REMARK 465 VAL A 594 REMARK 465 GLY A 595 REMARK 465 ALA A 596 REMARK 465 TYR A 597 REMARK 465 ARG A 598 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NH1 ARG A 210 O HOH A 801 1.81 REMARK 500 O HOH A 1242 O HOH A 1246 1.92 REMARK 500 O HOH A 1251 O HOH A 1268 2.03 REMARK 500 O HOH A 944 O HOH A 1178 2.06 REMARK 500 O HOH A 813 O HOH A 1207 2.06 REMARK 500 NE ARG A 210 O HOH A 802 2.10 REMARK 500 O HOH A 1047 O HOH A 1243 2.12 REMARK 500 O HOH A 1222 O HOH A 1241 2.16 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 MET A 464 CG - SD - CE ANGL. DEV. = -14.8 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 ARG A 78 -176.47 82.55 REMARK 500 ASP A 89 -6.95 77.39 REMARK 500 PRO A 96 -179.20 -63.37 REMARK 500 CYS A 130 54.22 -149.37 REMARK 500 ASP A 131 164.59 78.85 REMARK 500 THR A 132 32.45 -87.44 REMARK 500 LYS A 186 -127.04 50.39 REMARK 500 ASP A 187 34.90 -97.63 REMARK 500 THR A 266 53.40 -140.14 REMARK 500 SER A 287 -117.70 74.44 REMARK 500 TRP A 300 51.71 -107.75 REMARK 500 TRP A 326 -0.06 -140.16 REMARK 500 ASN A 379 -4.85 -140.58 REMARK 500 ASN A 420 -145.16 -104.28 REMARK 500 VAL A 458 -94.60 -107.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1297 DISTANCE = 6.33 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LA A 701 LA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 197 OE1 REMARK 620 2 GLU A 197 OE2 49.1 REMARK 620 3 ASN A 285 OD1 74.2 114.0 REMARK 620 4 ASP A 327 OD1 69.8 111.2 66.9 REMARK 620 5 ASP A 327 OD2 82.5 95.4 109.5 42.6 REMARK 620 6 ASP A 329 OD1 132.8 162.8 80.1 63.8 69.7 REMARK 620 7 ASP A 329 OD2 143.5 142.7 70.8 104.5 118.6 49.4 REMARK 620 8 PQQ A 702 O5 121.8 86.9 159.0 104.0 63.5 78.9 94.6 REMARK 620 9 PQQ A 702 N6 115.2 68.4 127.5 165.2 122.8 111.9 79.7 61.3 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 224 OD1 REMARK 620 2 GLY A 246 O 133.8 REMARK 620 3 SER A 249 OG 109.0 106.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LA A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PQQ A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 703 DBREF 6DAM A 1 617 PDB 6DAM 6DAM 1 617 SEQRES 1 A 617 MET LYS LYS PRO VAL LYS SER TRP LEU ILE ALA SER THR SEQRES 2 A 617 VAL ALA ALA LEU LEU ALA VAL PRO ALA VAL SER GLN ALA SEQRES 3 A 617 ASN SER GLU VAL GLU LYS LEU THR LYS ASN PRO ALA ASN SEQRES 4 A 617 TRP ALA THR TRP GLY GLY ASN TYR HIS GLY THR ARG TYR SEQRES 5 A 617 SER GLU LEU LYS GLN ILE ASN THR SER ASN VAL LYS ASN SEQRES 6 A 617 LEU GLN PRO ALA TRP THR PHE SER THR GLY VAL LEU ARG SEQRES 7 A 617 GLY HIS GLU GLY GLY PRO LEU VAL VAL ASN ASP VAL MET SEQRES 8 A 617 TYR ILE HIS THR PRO PHE PRO ASN THR VAL TYR ALA ILE SEQRES 9 A 617 ASP GLN LYS THR GLN ALA VAL ILE TRP GLU TYR THR PRO SEQRES 10 A 617 GLN GLN ASP ALA ASP VAL THR ILE PRO VAL MET CYS CYS SEQRES 11 A 617 ASP THR VAL ASN ARG GLY LEU ALA TYR GLY ASP GLY LYS SEQRES 12 A 617 ILE PHE LEU GLN GLN SER ASP THR VAL LEU THR ALA LEU SEQRES 13 A 617 ASP ALA LYS THR GLY LYS ARG VAL TRP SER VAL GLN ASN SEQRES 14 A 617 GLY ASP PRO LYS LEU GLY MET THR ASN THR GLN ALA PRO SEQRES 15 A 617 LEU VAL VAL LYS ASP LYS VAL ILE THR GLY ILE SER GLY SEQRES 16 A 617 GLY GLU PHE GLY VAL ARG GLY PHE LEU ALA ALA TYR ASN SEQRES 17 A 617 ILE ARG THR GLY GLU LEU ASP TRP LYS GLY TYR SER MET SEQRES 18 A 617 GLY PRO ASP ALA ASP THR LEU ILE ASN PRO THR LYS THR SEQRES 19 A 617 THR THR TRP LYS ASP GLY LYS VAL GLN PRO VAL GLY LYS SEQRES 20 A 617 ASP SER SER THR SER THR TRP GLU GLY ASP GLN TRP LYS SEQRES 21 A 617 ILE GLY GLY GLY THR THR TRP GLY TRP TYR SER TYR ASP SEQRES 22 A 617 PRO GLU LEU ASN LEU VAL TYR TYR GLY SER GLY ASN PRO SEQRES 23 A 617 SER THR TRP ASN PRO ALA GLN ARG PRO GLY ASP ASN LYS SEQRES 24 A 617 TRP SER MET SER LEU TRP ALA ARG ASN ALA ASP THR GLY SEQRES 25 A 617 GLU VAL LYS TRP VAL TYR GLN MET THR PRO HIS ASP GLU SEQRES 26 A 617 TRP ASP TYR ASP GLY ILE ASN GLU VAL ALA LEU VAL ASP SEQRES 27 A 617 GLN GLU ILE LYS GLY GLN MET ARG LYS THR ALA VAL HIS SEQRES 28 A 617 PHE ASP ARG ASN GLY PHE GLY TYR THR LEU ASP ARG VAL SEQRES 29 A 617 THR GLY GLU LEU LEU VAL ALA GLU LYS PHE ASP LYS ALA SEQRES 30 A 617 VAL ASN TRP ALA SER HIS VAL ASP MET LYS SER GLY ARG SEQRES 31 A 617 PRO GLN VAL VAL SER GLN TYR SER THR GLU TYR ASN GLY SEQRES 32 A 617 GLU ASP VAL ASN THR GLU GLY VAL CYS PRO ALA ALA LEU SEQRES 33 A 617 GLY SER LYS ASN GLN GLN PRO VAL SER TYR SER PRO GLN SEQRES 34 A 617 THR GLY TYR PHE TYR ILE SER GLY ASN HIS VAL CYS MET SEQRES 35 A 617 ASP TYR GLU PRO PHE GLU VAL GLU TYR THR ALA GLY GLN SEQRES 36 A 617 PRO TYR VAL GLY ALA THR LEU SER MET PHE PRO ALA GLY SEQRES 37 A 617 LYS ASP VAL ILE THR GLY LYS GLU ASP GLY SER ASN ASN SEQRES 38 A 617 LEU GLY GLN PHE THR ALA TRP ASP ALA THR THR GLY LYS SEQRES 39 A 617 ILE ILE TRP SER ASN LYS GLU GLN PHE SER VAL TRP SER SEQRES 40 A 617 GLY SER LEU ALA THR ALA GLY GLY VAL VAL PHE TYR GLY SEQRES 41 A 617 THR LEU GLU GLY TYR LEU LYS ALA VAL ASP ALA LYS THR SEQRES 42 A 617 GLY LYS GLU LEU TYR ARG PHE LYS THR PRO SER GLY ILE SEQRES 43 A 617 ILE GLY ASN VAL ASN THR TRP GLU TYR GLU GLY LYS GLN SEQRES 44 A 617 TYR VAL GLY VAL LEU SER GLY VAL GLY GLY TRP ALA GLY SEQRES 45 A 617 ILE GLY ILE ALA ALA GLY LEU ASP SER GLY GLU GLU SER SEQRES 46 A 617 SER ASN SER GLU GLY LEU GLY ALA VAL GLY ALA TYR ARG SEQRES 47 A 617 SER LEU SER SER TYR THR LYS LEU GLY GLY THR LEU THR SEQRES 48 A 617 VAL PHE ALA LEU PRO ASN HET LA A 701 1 HET PQQ A 702 24 HET NA A 703 1 HETNAM LA LANTHANUM (III) ION HETNAM PQQ PYRROLOQUINOLINE QUINONE HETNAM NA SODIUM ION FORMUL 2 LA LA 3+ FORMUL 3 PQQ C14 H6 N2 O8 FORMUL 4 NA NA 1+ FORMUL 5 HOH *497(H2 O) HELIX 1 AA1 ASN A 27 ASN A 36 1 10 HELIX 2 AA2 ASN A 62 LEU A 66 5 5 HELIX 3 AA3 ASP A 120 ILE A 125 1 6 HELIX 4 AA4 PRO A 126 MET A 128 5 3 HELIX 5 AA5 ASP A 171 GLY A 175 5 5 HELIX 6 AA6 PRO A 223 LEU A 228 1 6 HELIX 7 AA7 SER A 250 TRP A 254 5 5 HELIX 8 AA8 ASP A 257 GLY A 262 5 6 HELIX 9 AA9 ASN A 290 ARG A 294 5 5 HELIX 10 AB1 SER A 395 TYR A 397 5 3 HELIX 11 AB2 SER A 398 GLY A 403 1 6 HELIX 12 AB3 SER A 599 TYR A 603 5 5 SHEET 1 AA1 5 TYR A 52 SER A 53 0 SHEET 2 AA1 5 LEU A 510 THR A 512 1 O ALA A 511 N SER A 53 SHEET 3 AA1 5 VAL A 516 GLY A 520 -1 O PHE A 518 N LEU A 510 SHEET 4 AA1 5 TYR A 525 ASP A 530 -1 O LYS A 527 N TYR A 519 SHEET 5 AA1 5 GLU A 536 LYS A 541 -1 O LEU A 537 N ALA A 528 SHEET 1 AA2 4 GLN A 67 SER A 73 0 SHEET 2 AA2 4 THR A 609 ALA A 614 -1 O VAL A 612 N ALA A 69 SHEET 3 AA2 4 LYS A 558 SER A 565 -1 N VAL A 561 O PHE A 613 SHEET 4 AA2 4 ASN A 551 TYR A 555 -1 N ASN A 551 O GLY A 562 SHEET 1 AA3 4 LEU A 85 VAL A 87 0 SHEET 2 AA3 4 VAL A 90 HIS A 94 -1 O TYR A 92 N LEU A 85 SHEET 3 AA3 4 VAL A 101 ASP A 105 -1 O ILE A 104 N MET A 91 SHEET 4 AA3 4 ALA A 110 TYR A 115 -1 O ILE A 112 N ALA A 103 SHEET 1 AA4 4 ALA A 138 GLY A 140 0 SHEET 2 AA4 4 LYS A 143 GLN A 147 -1 O PHE A 145 N ALA A 138 SHEET 3 AA4 4 VAL A 152 ASP A 157 -1 O LEU A 156 N ILE A 144 SHEET 4 AA4 4 ARG A 163 GLN A 168 -1 O VAL A 164 N ALA A 155 SHEET 1 AA5 4 LEU A 183 VAL A 185 0 SHEET 2 AA5 4 LYS A 188 THR A 191 -1 O ILE A 190 N LEU A 183 SHEET 3 AA5 4 PHE A 203 ASN A 208 -1 O ALA A 205 N THR A 191 SHEET 4 AA5 4 LEU A 214 TYR A 219 -1 O GLY A 218 N LEU A 204 SHEET 1 AA6 2 THR A 235 LYS A 238 0 SHEET 2 AA6 2 LYS A 241 PRO A 244 -1 O GLN A 243 N THR A 236 SHEET 1 AA7 4 SER A 271 ASP A 273 0 SHEET 2 AA7 4 LEU A 278 GLY A 282 -1 O TYR A 280 N SER A 271 SHEET 3 AA7 4 SER A 303 ASN A 308 -1 O ARG A 307 N VAL A 279 SHEET 4 AA7 4 VAL A 314 GLN A 319 -1 O LYS A 315 N ALA A 306 SHEET 1 AA8 4 ALA A 335 ILE A 341 0 SHEET 2 AA8 4 GLN A 344 PHE A 352 -1 O ARG A 346 N GLN A 339 SHEET 3 AA8 4 PHE A 357 ASP A 362 -1 O TYR A 359 N HIS A 351 SHEET 4 AA8 4 LEU A 368 LYS A 373 -1 O GLU A 372 N GLY A 358 SHEET 1 AA9 2 ALA A 381 VAL A 384 0 SHEET 2 AA9 2 PRO A 391 VAL A 393 -1 O GLN A 392 N HIS A 383 SHEET 1 AB1 3 THR A 408 VAL A 411 0 SHEET 2 AB1 3 VAL A 440 PRO A 446 -1 O TYR A 444 N THR A 408 SHEET 3 AB1 3 ALA A 460 PRO A 466 -1 O PHE A 465 N CYS A 441 SHEET 1 AB2 4 SER A 425 SER A 427 0 SHEET 2 AB2 4 TYR A 432 ASN A 438 -1 O TYR A 434 N SER A 425 SHEET 3 AB2 4 GLY A 483 ASP A 489 -1 O THR A 486 N ILE A 435 SHEET 4 AB2 4 LYS A 494 GLU A 501 -1 O ILE A 496 N ALA A 487 SSBOND 1 CYS A 129 CYS A 130 1555 1555 2.10 SSBOND 2 CYS A 412 CYS A 441 1555 1555 2.04 LINK OE1 GLU A 197 LA LA A 701 1555 1555 2.61 LINK OE2 GLU A 197 LA LA A 701 1555 1555 2.69 LINK OD1 ASP A 224 NA NA A 703 1555 1555 2.93 LINK O GLY A 246 NA NA A 703 1555 1555 2.69 LINK OG SER A 249 NA NA A 703 1555 1555 2.90 LINK OD1 ASN A 285 LA LA A 701 1555 1555 2.59 LINK OD1 ASP A 327 LA LA A 701 1555 1555 2.75 LINK OD2 ASP A 327 LA LA A 701 1555 1555 3.15 LINK OD1 ASP A 329 LA LA A 701 1555 1555 2.54 LINK OD2 ASP A 329 LA LA A 701 1555 1555 2.69 LINK LA LA A 701 O5 PQQ A 702 1555 1555 2.61 LINK LA LA A 701 N6 PQQ A 702 1555 1555 2.77 LINK LA LA A 701 O7A PQQ A 702 1555 1555 2.53 CISPEP 1 PHE A 97 PRO A 98 0 6.49 CISPEP 2 LYS A 299 TRP A 300 0 -1.80 CISPEP 3 CYS A 412 PRO A 413 0 3.50 SITE 1 AC1 5 GLU A 197 ASN A 285 ASP A 327 ASP A 329 SITE 2 AC1 5 PQQ A 702 SITE 1 AC2 23 GLU A 81 CYS A 129 CYS A 130 ARG A 135 SITE 2 AC2 23 THR A 179 SER A 194 GLY A 195 GLY A 196 SITE 3 AC2 23 GLU A 197 THR A 265 TRP A 267 ASN A 285 SITE 4 AC2 23 ASP A 327 ASP A 329 ARG A 354 ASN A 420 SITE 5 AC2 23 TRP A 506 GLY A 569 TRP A 570 LA A 701 SITE 6 AC2 23 HOH A 834 HOH A1062 HOH A1103 SITE 1 AC3 5 ASP A 224 GLY A 246 LYS A 247 ASP A 248 SITE 2 AC3 5 SER A 249 CRYST1 55.347 92.283 191.772 90.00 90.00 90.00 C 2 2 21 8 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 0.018068 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005215 0.00000