HEADER OXIDOREDUCTASE 12-APR-19 6OJR TITLE CRYSTAL STRUCTURE OF SPHINGOMONAS PAUCIMOBILIS TMY1009 APO-LSDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGNOSTILBENE-ALPHA,BETA-DIOXYGENASE ISOZYME I; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LSD-I; COMPND 5 EC: 1.13.11.43; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPHINGOMONAS PAUCIMOBILIS; SOURCE 3 ORGANISM_TAXID: 13689; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET41B KEYWDS AROMATIC COMPOUND, LIGNOSTILBENE, CAROTENOID CLEAVAGE OXYGENASE, KEYWDS 2 LIGNIN DEGRADATION, BACTERIAL CATABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR E.KUATSJAH,M.M.VERSTRAETE,M.J.KOBYLARZ,A.K.N.LIU,M.E.P.MURPHY, AUTHOR 2 L.D.ELTIS REVDAT 4 11-OCT-23 6OJR 1 REMARK REVDAT 3 08-JAN-20 6OJR 1 REMARK REVDAT 2 11-SEP-19 6OJR 1 JRNL REVDAT 1 24-JUL-19 6OJR 0 JRNL AUTH E.KUATSJAH,M.M.VERSTRAETE,M.J.KOBYLARZ,A.K.N.LIU, JRNL AUTH 2 M.E.P.MURPHY,L.D.ELTIS JRNL TITL IDENTIFICATION OF FUNCTIONALLY IMPORTANT RESIDUES AND JRNL TITL 2 STRUCTURAL FEATURES IN A BACTERIAL LIGNOSTILBENE JRNL TITL 3 DIOXYGENASE. JRNL REF J.BIOL.CHEM. V. 294 12911 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31292192 JRNL DOI 10.1074/JBC.RA119.009428 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 155094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 3874 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 39.2722 - 6.9708 1.00 5421 133 0.1730 0.1761 REMARK 3 2 6.9708 - 5.5379 1.00 5397 140 0.1618 0.1864 REMARK 3 3 5.5379 - 4.8393 1.00 5427 140 0.1375 0.1269 REMARK 3 4 4.8393 - 4.3975 1.00 5410 138 0.1236 0.1464 REMARK 3 5 4.3975 - 4.0827 1.00 5389 146 0.1328 0.1519 REMARK 3 6 4.0827 - 3.8422 1.00 5411 140 0.1407 0.1757 REMARK 3 7 3.8422 - 3.6499 1.00 5371 140 0.1521 0.1900 REMARK 3 8 3.6499 - 3.4911 1.00 5438 138 0.1705 0.2016 REMARK 3 9 3.4911 - 3.3568 1.00 5406 132 0.1773 0.1940 REMARK 3 10 3.3568 - 3.2410 1.00 5378 138 0.1840 0.2407 REMARK 3 11 3.2410 - 3.1397 1.00 5439 140 0.1859 0.1930 REMARK 3 12 3.1397 - 3.0500 1.00 5391 138 0.1925 0.2249 REMARK 3 13 3.0500 - 2.9697 1.00 5396 137 0.1978 0.2136 REMARK 3 14 2.9697 - 2.8973 1.00 5466 140 0.2066 0.2309 REMARK 3 15 2.8973 - 2.8315 1.00 5429 137 0.2123 0.2484 REMARK 3 16 2.8315 - 2.7712 1.00 5377 136 0.2139 0.2352 REMARK 3 17 2.7712 - 2.7158 1.00 5377 140 0.2167 0.2629 REMARK 3 18 2.7158 - 2.6646 1.00 5419 142 0.2230 0.2674 REMARK 3 19 2.6646 - 2.6170 1.00 5437 142 0.2252 0.2231 REMARK 3 20 2.6170 - 2.5726 1.00 5393 136 0.2378 0.2588 REMARK 3 21 2.5726 - 2.5311 1.00 5415 134 0.2441 0.3142 REMARK 3 22 2.5311 - 2.4922 1.00 5371 138 0.2591 0.3325 REMARK 3 23 2.4922 - 2.4556 1.00 5442 138 0.2665 0.2680 REMARK 3 24 2.4556 - 2.4210 1.00 5396 142 0.2712 0.3069 REMARK 3 25 2.4210 - 2.3883 1.00 5401 134 0.2688 0.2848 REMARK 3 26 2.3883 - 2.3573 1.00 5399 138 0.2805 0.2884 REMARK 3 27 2.3573 - 2.3278 1.00 5353 140 0.2779 0.2911 REMARK 3 28 2.3278 - 2.2997 0.97 5271 137 0.2943 0.2948 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.76 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 : 0.002 7854 REMARK 3 ANGLE : 0.615 10661 REMARK 3 CHIRALITY : 0.046 1097 REMARK 3 PLANARITY : 0.003 1420 REMARK 3 DIHEDRAL : 11.685 4619 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6OJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000240659. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12709 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 155094 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 39.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 13.00 REMARK 200 R MERGE FOR SHELL (I) : 1.46500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 2BIW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRI-POTASSIUM CITRATE, 20% REMARK 280 PEG3350 (V/V), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.32200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.66100 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.66100 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.32200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 GLY A 381 REMARK 465 GLY A 382 REMARK 465 ALA A 383 REMARK 465 PHE A 384 REMARK 465 ALA B 483 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 385 CG CD1 CD2 CE1 CE2 CZ OH 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 OE2 GLU A 135 HD1 HIS A 218 1.42 REMARK 500 OE2 GLU B 135 HD1 HIS B 218 1.47 REMARK 500 HH22 ARG B 353 O GLY B 473 1.56 REMARK 500 HH22 ARG A 353 O GLY A 473 1.59 REMARK 500 HE22 GLN A 469 MG MG A 506 1.59 REMARK 500 NH2 ARG A 353 O GLY A 473 2.07 REMARK 500 O HOH A 856 O HOH A 861 2.09 REMARK 500 OD2 ASP B 437 O HOH B 601 2.10 REMARK 500 NH2 ARG B 353 O GLY B 473 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 336 HH12 ARG B 301 5565 1.60 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 GLN A 6 41.57 -89.40 REMARK 500 LEU A 17 -73.63 -111.15 REMARK 500 ASP A 25 76.50 63.04 REMARK 500 ASP A 46 76.11 -155.41 REMARK 500 HIS A 167 57.45 -141.29 REMARK 500 HIS A 452 53.96 -145.28 REMARK 500 LEU A 471 -105.95 -119.60 REMARK 500 GLN B 6 44.49 -94.61 REMARK 500 LEU B 17 -71.62 -107.94 REMARK 500 ASP B 25 74.10 61.69 REMARK 500 ASP B 46 79.26 -155.26 REMARK 500 HIS B 71 132.91 -175.35 REMARK 500 HIS B 167 57.16 -140.22 REMARK 500 ALA B 383 30.98 70.37 REMARK 500 HIS B 452 53.03 -144.54 REMARK 500 PRO B 464 30.38 -82.81 REMARK 500 LEU B 471 -105.36 -119.07 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 356 OE2 REMARK 620 2 HOH A 750 O 123.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 372 OD2 REMARK 620 2 THR A 390 OG1 119.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 DBREF 6OJR A 2 483 UNP Q53353 LSDX1_SPHPI 2 483 DBREF 6OJR B 2 483 UNP Q53353 LSDX1_SPHPI 2 483 SEQADV 6OJR ALA A 483 UNP Q53353 VAL 483 CONFLICT SEQADV 6OJR ALA B 483 UNP Q53353 VAL 483 CONFLICT SEQRES 1 A 482 ALA HIS PHE PRO GLN THR PRO GLY PHE SER GLY THR LEU SEQRES 2 A 482 ARG PRO LEU ARG ILE GLU GLY ASP ILE LEU ASP ILE GLU SEQRES 3 A 482 ILE GLU GLY GLU VAL PRO PRO GLN LEU ASN GLY THR PHE SEQRES 4 A 482 HIS ARG VAL HIS PRO ASP ALA GLN PHE PRO PRO ARG PHE SEQRES 5 A 482 GLU ASP ASP GLN PHE PHE ASN GLY ASP GLY MET VAL SER SEQRES 6 A 482 LEU PHE ARG PHE HIS ASP GLY LYS ILE ASP PHE ARG GLN SEQRES 7 A 482 ARG TYR ALA GLN THR ASP LYS TRP LYS VAL GLU ARG LYS SEQRES 8 A 482 ALA GLY LYS SER LEU PHE GLY ALA TYR ARG ASN PRO LEU SEQRES 9 A 482 THR ASP ASP ALA SER VAL GLN GLY MET ILE ARG GLY THR SEQRES 10 A 482 ALA ASN THR ASN VAL MET VAL HIS ALA GLY LYS LEU TYR SEQRES 11 A 482 ALA MET LYS GLU ASP SER PRO CYS LEU ILE MET ASP PRO SEQRES 12 A 482 LEU THR LEU GLU THR GLU GLY TYR THR ASN PHE ASP GLY SEQRES 13 A 482 LYS LEU GLN SER GLN THR PHE CYS ALA HIS PRO LYS ILE SEQRES 14 A 482 ASP PRO VAL THR GLY ASN LEU CYS ALA PHE ALA TYR GLY SEQRES 15 A 482 ALA LYS GLY LEU MET THR LEU ASP MET ALA TYR ILE GLU SEQRES 16 A 482 ILE SER PRO THR GLY LYS LEU LEU LYS GLU ILE PRO PHE SEQRES 17 A 482 GLN ASN PRO TYR TYR CYS MET MET HIS ASP PHE GLY VAL SEQRES 18 A 482 THR GLU ASP TYR ALA VAL PHE ALA VAL MET PRO LEU LEU SEQRES 19 A 482 SER SER TRP ASP ARG LEU GLU GLN ARG LEU PRO PHE PHE SEQRES 20 A 482 GLY PHE ASP THR THR LEU PRO CYS TYR LEU GLY ILE LEU SEQRES 21 A 482 PRO ARG ASN GLY ASP ALA ARG ASP LEU ARG TRP PHE LYS SEQRES 22 A 482 THR GLY ASN CYS PHE VAL GLY HIS VAL MET ASN ALA PHE SEQRES 23 A 482 ASN ASP GLY THR LYS VAL HIS ILE ASP MET PRO VAL SER SEQRES 24 A 482 ARG ASN ASN SER PHE PRO PHE PHE ASP VAL HIS GLY ALA SEQRES 25 A 482 PRO PHE ASP PRO VAL ALA GLY GLN GLY PHE LEU THR ARG SEQRES 26 A 482 TRP THR VAL ASP MET ALA SER ASN GLY ASP SER PHE GLU SEQRES 27 A 482 LYS THR GLU ARG LEU PHE ASP ARG PRO ASP GLU PHE PRO SEQRES 28 A 482 ARG ILE ASP GLU ARG TYR ALA THR ARG ALA TYR ARG HIS SEQRES 29 A 482 GLY TRP MET LEU ILE LEU ASP THR GLU LYS PRO TYR GLU SEQRES 30 A 482 ALA PRO GLY GLY ALA PHE TYR ALA LEU THR ASN THR LEU SEQRES 31 A 482 GLY HIS ILE ASP LEU ALA THR GLY LYS SER SER SER TRP SEQRES 32 A 482 TRP ALA GLY PRO ARG CYS ALA ILE GLN GLU PRO CYS PHE SEQRES 33 A 482 ILE PRO ARG SER PRO ASP ALA PRO GLU GLY ASP GLY TYR SEQRES 34 A 482 VAL ILE ALA LEU VAL ASP ASP HIS VAL ALA ASN TYR SER SEQRES 35 A 482 ASP LEU ALA ILE PHE ASP ALA GLN HIS VAL ASP GLN GLY SEQRES 36 A 482 PRO ILE ALA ARG ALA LYS LEU PRO VAL ARG ILE ARG GLN SEQRES 37 A 482 GLY LEU HIS GLY ASN TRP ALA ASP ALA SER ARG LEU ALA SEQRES 38 A 482 ALA SEQRES 1 B 482 ALA HIS PHE PRO GLN THR PRO GLY PHE SER GLY THR LEU SEQRES 2 B 482 ARG PRO LEU ARG ILE GLU GLY ASP ILE LEU ASP ILE GLU SEQRES 3 B 482 ILE GLU GLY GLU VAL PRO PRO GLN LEU ASN GLY THR PHE SEQRES 4 B 482 HIS ARG VAL HIS PRO ASP ALA GLN PHE PRO PRO ARG PHE SEQRES 5 B 482 GLU ASP ASP GLN PHE PHE ASN GLY ASP GLY MET VAL SER SEQRES 6 B 482 LEU PHE ARG PHE HIS ASP GLY LYS ILE ASP PHE ARG GLN SEQRES 7 B 482 ARG TYR ALA GLN THR ASP LYS TRP LYS VAL GLU ARG LYS SEQRES 8 B 482 ALA GLY LYS SER LEU PHE GLY ALA TYR ARG ASN PRO LEU SEQRES 9 B 482 THR ASP ASP ALA SER VAL GLN GLY MET ILE ARG GLY THR SEQRES 10 B 482 ALA ASN THR ASN VAL MET VAL HIS ALA GLY LYS LEU TYR SEQRES 11 B 482 ALA MET LYS GLU ASP SER PRO CYS LEU ILE MET ASP PRO SEQRES 12 B 482 LEU THR LEU GLU THR GLU GLY TYR THR ASN PHE ASP GLY SEQRES 13 B 482 LYS LEU GLN SER GLN THR PHE CYS ALA HIS PRO LYS ILE SEQRES 14 B 482 ASP PRO VAL THR GLY ASN LEU CYS ALA PHE ALA TYR GLY SEQRES 15 B 482 ALA LYS GLY LEU MET THR LEU ASP MET ALA TYR ILE GLU SEQRES 16 B 482 ILE SER PRO THR GLY LYS LEU LEU LYS GLU ILE PRO PHE SEQRES 17 B 482 GLN ASN PRO TYR TYR CYS MET MET HIS ASP PHE GLY VAL SEQRES 18 B 482 THR GLU ASP TYR ALA VAL PHE ALA VAL MET PRO LEU LEU SEQRES 19 B 482 SER SER TRP ASP ARG LEU GLU GLN ARG LEU PRO PHE PHE SEQRES 20 B 482 GLY PHE ASP THR THR LEU PRO CYS TYR LEU GLY ILE LEU SEQRES 21 B 482 PRO ARG ASN GLY ASP ALA ARG ASP LEU ARG TRP PHE LYS SEQRES 22 B 482 THR GLY ASN CYS PHE VAL GLY HIS VAL MET ASN ALA PHE SEQRES 23 B 482 ASN ASP GLY THR LYS VAL HIS ILE ASP MET PRO VAL SER SEQRES 24 B 482 ARG ASN ASN SER PHE PRO PHE PHE ASP VAL HIS GLY ALA SEQRES 25 B 482 PRO PHE ASP PRO VAL ALA GLY GLN GLY PHE LEU THR ARG SEQRES 26 B 482 TRP THR VAL ASP MET ALA SER ASN GLY ASP SER PHE GLU SEQRES 27 B 482 LYS THR GLU ARG LEU PHE ASP ARG PRO ASP GLU PHE PRO SEQRES 28 B 482 ARG ILE ASP GLU ARG TYR ALA THR ARG ALA TYR ARG HIS SEQRES 29 B 482 GLY TRP MET LEU ILE LEU ASP THR GLU LYS PRO TYR GLU SEQRES 30 B 482 ALA PRO GLY GLY ALA PHE TYR ALA LEU THR ASN THR LEU SEQRES 31 B 482 GLY HIS ILE ASP LEU ALA THR GLY LYS SER SER SER TRP SEQRES 32 B 482 TRP ALA GLY PRO ARG CYS ALA ILE GLN GLU PRO CYS PHE SEQRES 33 B 482 ILE PRO ARG SER PRO ASP ALA PRO GLU GLY ASP GLY TYR SEQRES 34 B 482 VAL ILE ALA LEU VAL ASP ASP HIS VAL ALA ASN TYR SER SEQRES 35 B 482 ASP LEU ALA ILE PHE ASP ALA GLN HIS VAL ASP GLN GLY SEQRES 36 B 482 PRO ILE ALA ARG ALA LYS LEU PRO VAL ARG ILE ARG GLN SEQRES 37 B 482 GLY LEU HIS GLY ASN TRP ALA ASP ALA SER ARG LEU ALA SEQRES 38 B 482 ALA HET GOL A 501 14 HET GOL A 502 14 HET GOL A 503 14 HET MG A 504 1 HET MG A 505 1 HET MG A 506 1 HET GOL B 501 14 HET GOL B 502 14 HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 5(C3 H8 O3) FORMUL 6 MG 3(MG 2+) FORMUL 11 HOH *547(H2 O) HELIX 1 AA1 THR A 7 ARG A 15 5 9 HELIX 2 AA2 GLN A 57 GLY A 61 5 5 HELIX 3 AA3 THR A 84 GLY A 94 1 11 HELIX 4 AA4 ASN A 103 ASP A 107 5 5 HELIX 5 AA5 ASP A 108 GLN A 112 5 5 HELIX 6 AA6 SER A 237 GLN A 243 1 7 HELIX 7 AA7 ASP A 266 LEU A 270 5 5 HELIX 8 AA8 GLU A 356 ALA A 359 5 4 HELIX 9 AA9 HIS A 452 GLY A 456 5 5 HELIX 10 AB1 SER A 479 LEU A 481 5 3 HELIX 11 AB2 THR B 7 ARG B 15 5 9 HELIX 12 AB3 GLN B 57 GLY B 61 5 5 HELIX 13 AB4 THR B 84 GLY B 94 1 11 HELIX 14 AB5 ASN B 103 ASP B 107 5 5 HELIX 15 AB6 ASP B 108 GLN B 112 5 5 HELIX 16 AB7 SER B 237 GLN B 243 1 7 HELIX 17 AB8 ASP B 266 LEU B 270 5 5 HELIX 18 AB9 GLU B 356 ALA B 359 5 4 HELIX 19 AC1 HIS B 452 GLY B 456 5 5 HELIX 20 AC2 SER B 479 LEU B 481 5 3 SHEET 1 AA110 GLY A 473 ASP A 477 0 SHEET 2 AA110 ASN A 37 PRO A 45 -1 N THR A 39 O ALA A 476 SHEET 3 AA110 GLY A 63 HIS A 71 -1 O SER A 66 N ARG A 42 SHEET 4 AA110 LYS A 74 TYR A 81 -1 O ARG A 78 N LEU A 67 SHEET 5 AA110 GLU A 20 ILE A 23 -1 N ILE A 23 O PHE A 77 SHEET 6 AA110 GLU B 20 ILE B 23 -1 O GLU B 20 N ASP A 22 SHEET 7 AA110 LYS B 74 TYR B 81 -1 O PHE B 77 N ILE B 23 SHEET 8 AA110 GLY B 63 HIS B 71 -1 N LEU B 67 O ARG B 78 SHEET 9 AA110 GLY B 38 PRO B 45 -1 N ARG B 42 O SER B 66 SHEET 10 AA110 GLY B 473 ASP B 477 -1 O ALA B 476 N THR B 39 SHEET 1 AA2 5 GLU A 27 GLY A 30 0 SHEET 2 AA2 5 ALA A 459 LYS A 462 -1 O ARG A 460 N GLU A 29 SHEET 3 AA2 5 TYR A 442 ASP A 449 -1 N ILE A 447 O ALA A 459 SHEET 4 AA2 5 GLY A 429 ASP A 437 -1 N VAL A 435 O ASP A 444 SHEET 5 AA2 5 CYS A 410 ILE A 412 -1 N ALA A 411 O ASP A 436 SHEET 1 AA3 5 GLU A 27 GLY A 30 0 SHEET 2 AA3 5 ALA A 459 LYS A 462 -1 O ARG A 460 N GLU A 29 SHEET 3 AA3 5 TYR A 442 ASP A 449 -1 N ILE A 447 O ALA A 459 SHEET 4 AA3 5 GLY A 429 ASP A 437 -1 N VAL A 435 O ASP A 444 SHEET 5 AA3 5 CYS A 416 PRO A 419 -1 N ILE A 418 O TYR A 430 SHEET 1 AA4 4 ASN A 122 HIS A 126 0 SHEET 2 AA4 4 LYS A 129 MET A 133 -1 O TYR A 131 N MET A 124 SHEET 3 AA4 4 CYS A 139 MET A 142 -1 O LEU A 140 N ALA A 132 SHEET 4 AA4 4 THR A 149 THR A 153 -1 O GLU A 150 N ILE A 141 SHEET 1 AA5 4 LYS A 169 ILE A 170 0 SHEET 2 AA5 4 LEU A 177 TYR A 182 -1 O CYS A 178 N LYS A 169 SHEET 3 AA5 4 ASP A 191 ILE A 197 -1 O ILE A 195 N ALA A 179 SHEET 4 AA5 4 LEU A 203 GLN A 210 -1 O PHE A 209 N MET A 192 SHEET 1 AA6 4 GLY A 221 VAL A 222 0 SHEET 2 AA6 4 TYR A 226 VAL A 231 -1 O VAL A 228 N GLY A 221 SHEET 3 AA6 4 CYS A 256 PRO A 262 -1 O TYR A 257 N VAL A 231 SHEET 4 AA6 4 ARG A 271 THR A 275 -1 O ARG A 271 N ILE A 260 SHEET 1 AA7 2 LEU A 234 SER A 236 0 SHEET 2 AA7 2 PHE A 248 PHE A 250 -1 O GLY A 249 N LEU A 235 SHEET 1 AA8 3 PHE A 279 VAL A 280 0 SHEET 2 AA8 3 LYS A 292 SER A 300 -1 O SER A 300 N PHE A 279 SHEET 3 AA8 3 ASN A 285 ASP A 289 -1 N ASP A 289 O LYS A 292 SHEET 1 AA9 4 PHE A 279 VAL A 280 0 SHEET 2 AA9 4 LYS A 292 SER A 300 -1 O SER A 300 N PHE A 279 SHEET 3 AA9 4 PHE A 323 ASP A 330 -1 O VAL A 329 N VAL A 293 SHEET 4 AA9 4 LYS A 340 ARG A 343 -1 O GLU A 342 N ARG A 326 SHEET 1 AB1 4 ASP A 349 ILE A 354 0 SHEET 2 AB1 4 HIS A 365 ILE A 370 -1 O LEU A 369 N GLU A 350 SHEET 3 AB1 4 THR A 390 ASP A 395 -1 O GLY A 392 N MET A 368 SHEET 4 AB1 4 SER A 401 TRP A 405 -1 O SER A 402 N HIS A 393 SHEET 1 AB2 5 GLU B 27 GLY B 30 0 SHEET 2 AB2 5 ALA B 459 LEU B 463 -1 O ARG B 460 N GLU B 29 SHEET 3 AB2 5 TYR B 442 ASP B 449 -1 N ILE B 447 O ALA B 459 SHEET 4 AB2 5 GLY B 429 ASP B 437 -1 N VAL B 435 O ASP B 444 SHEET 5 AB2 5 CYS B 410 ILE B 412 -1 N ALA B 411 O ASP B 436 SHEET 1 AB3 5 GLU B 27 GLY B 30 0 SHEET 2 AB3 5 ALA B 459 LEU B 463 -1 O ARG B 460 N GLU B 29 SHEET 3 AB3 5 TYR B 442 ASP B 449 -1 N ILE B 447 O ALA B 459 SHEET 4 AB3 5 GLY B 429 ASP B 437 -1 N VAL B 435 O ASP B 444 SHEET 5 AB3 5 CYS B 416 PRO B 419 -1 N ILE B 418 O TYR B 430 SHEET 1 AB4 4 ASN B 122 HIS B 126 0 SHEET 2 AB4 4 LYS B 129 MET B 133 -1 O TYR B 131 N MET B 124 SHEET 3 AB4 4 CYS B 139 MET B 142 -1 O MET B 142 N LEU B 130 SHEET 4 AB4 4 THR B 149 THR B 153 -1 O GLU B 150 N ILE B 141 SHEET 1 AB5 4 LYS B 169 ILE B 170 0 SHEET 2 AB5 4 LEU B 177 TYR B 182 -1 O CYS B 178 N LYS B 169 SHEET 3 AB5 4 ASP B 191 ILE B 197 -1 O ILE B 195 N ALA B 179 SHEET 4 AB5 4 LEU B 203 GLN B 210 -1 O PHE B 209 N MET B 192 SHEET 1 AB6 4 GLY B 221 VAL B 222 0 SHEET 2 AB6 4 TYR B 226 VAL B 231 -1 O VAL B 228 N GLY B 221 SHEET 3 AB6 4 CYS B 256 PRO B 262 -1 O TYR B 257 N VAL B 231 SHEET 4 AB6 4 ARG B 271 THR B 275 -1 O ARG B 271 N ILE B 260 SHEET 1 AB7 2 LEU B 234 SER B 236 0 SHEET 2 AB7 2 PHE B 248 PHE B 250 -1 O GLY B 249 N LEU B 235 SHEET 1 AB8 3 PHE B 279 VAL B 280 0 SHEET 2 AB8 3 LYS B 292 SER B 300 -1 O SER B 300 N PHE B 279 SHEET 3 AB8 3 ASN B 285 ASP B 289 -1 N ASP B 289 O LYS B 292 SHEET 1 AB9 4 PHE B 279 VAL B 280 0 SHEET 2 AB9 4 LYS B 292 SER B 300 -1 O SER B 300 N PHE B 279 SHEET 3 AB9 4 PHE B 323 ASP B 330 -1 O VAL B 329 N VAL B 293 SHEET 4 AB9 4 LYS B 340 ARG B 343 -1 O GLU B 342 N ARG B 326 SHEET 1 AC1 4 ASP B 349 ILE B 354 0 SHEET 2 AC1 4 HIS B 365 ILE B 370 -1 O TRP B 367 N ARG B 353 SHEET 3 AC1 4 THR B 390 ASP B 395 -1 O GLY B 392 N MET B 368 SHEET 4 AC1 4 SER B 401 TRP B 405 -1 O SER B 402 N HIS B 393 LINK OE2 GLU A 356 MG MG A 505 1555 1555 2.37 LINK OD2 ASP A 372 MG MG A 504 1555 1555 2.29 LINK OG1 THR A 390 MG MG A 504 1555 1555 2.75 LINK O ILE A 412 MG MG A 506 1555 1555 2.81 LINK MG MG A 505 O HOH A 750 1555 1555 2.65 SITE 1 AC1 6 ALA A 127 LYS A 129 TYR A 131 THR A 153 SITE 2 AC1 6 PHE A 155 THR A 200 SITE 1 AC2 1 HOH A 619 SITE 1 AC3 3 ALA A 2 HIS A 3 PRO A 50 SITE 1 AC4 4 ARG A 347 ASP A 372 LYS A 375 THR A 390 SITE 1 AC5 4 ARG A 353 ILE A 354 GLU A 356 HOH A 750 SITE 1 AC6 4 THR A 388 ALA A 411 ILE A 412 GLN A 469 SITE 1 AC7 5 TYR B 101 ARG B 102 THR B 121 LYS B 134 SITE 2 AC7 5 GLU B 135 CRYST1 181.364 181.364 94.983 90.00 90.00 120.00 P 32 2 1 12 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 0.005514 0.003183 0.000000 0.00000 SCALE2 0.000000 0.006367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010528 0.00000