HEADER OXIDOREDUCTASE 12-APR-19 6OJW TITLE CRYSTAL STRUCTURE OF SPHINGOMONAS PAUCIMOBILIS TMY1009 HOLO-LSDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGNOSTILBENE-ALPHA,BETA-DIOXYGENASE ISOZYME I; COMPND 3 CHAIN: B, A; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 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 13-MAR-24 6OJW 1 LINK REVDAT 3 08-JAN-20 6OJW 1 REMARK REVDAT 2 11-SEP-19 6OJW 1 JRNL REVDAT 1 24-JUL-19 6OJW 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 56612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2872 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 79.3904 - 7.1716 0.99 2692 138 0.1918 0.2141 REMARK 3 2 7.1716 - 5.6928 1.00 2604 148 0.1850 0.1986 REMARK 3 3 5.6928 - 4.9734 1.00 2582 139 0.1501 0.1705 REMARK 3 4 4.9734 - 4.5187 1.00 2586 129 0.1329 0.1492 REMARK 3 5 4.5187 - 4.1948 1.00 2569 137 0.1376 0.1475 REMARK 3 6 4.1948 - 3.9475 1.00 2577 123 0.1500 0.1636 REMARK 3 7 3.9475 - 3.7498 1.00 2559 143 0.1626 0.1923 REMARK 3 8 3.7498 - 3.5866 1.00 2575 127 0.1747 0.2160 REMARK 3 9 3.5866 - 3.4485 1.00 2558 129 0.1995 0.2027 REMARK 3 10 3.4485 - 3.3295 1.00 2551 121 0.1940 0.2291 REMARK 3 11 3.3295 - 3.2254 1.00 2544 130 0.1996 0.2586 REMARK 3 12 3.2254 - 3.1332 1.00 2548 158 0.2073 0.2664 REMARK 3 13 3.1332 - 3.0507 1.00 2522 158 0.2199 0.2778 REMARK 3 14 3.0507 - 2.9763 1.00 2510 151 0.2242 0.2658 REMARK 3 15 2.9763 - 2.9086 1.00 2541 133 0.2299 0.2572 REMARK 3 16 2.9086 - 2.8467 1.00 2564 126 0.2460 0.3085 REMARK 3 17 2.8467 - 2.7898 1.00 2515 149 0.2476 0.2783 REMARK 3 18 2.7898 - 2.7371 1.00 2527 133 0.2523 0.2607 REMARK 3 19 2.7371 - 2.6882 0.99 2525 143 0.2591 0.2734 REMARK 3 20 2.6882 - 2.6427 1.00 2521 118 0.2619 0.2709 REMARK 3 21 2.6427 - 2.6000 0.99 2570 139 0.2849 0.3239 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.87 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 : 0.003 7731 REMARK 3 ANGLE : 0.609 10493 REMARK 3 CHIRALITY : 0.046 1082 REMARK 3 PLANARITY : 0.004 1397 REMARK 3 DIHEDRAL : 13.099 4554 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 6OJW 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_1000240709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-15 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) : 1.12708 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 91.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 1.00700 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 2.7.16 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 25% PEG3350 REMARK 280 (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 63.38733 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 31.69367 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 31.69367 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 63.38733 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: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 A 759 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 PRO B 306 REMARK 465 PHE B 307 REMARK 465 PHE B 308 REMARK 465 ASP B 309 REMARK 465 VAL B 310 REMARK 465 HIS B 311 REMARK 465 GLY B 312 REMARK 465 ALA B 313 REMARK 465 PRO B 314 REMARK 465 PHE B 315 REMARK 465 GLY B 381 REMARK 465 GLY B 382 REMARK 465 ALA B 383 REMARK 465 PHE B 384 REMARK 465 TYR B 385 REMARK 465 ALA B 386 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 1.41 REMARK 500 OE2 GLU B 135 HD1 HIS B 218 1.43 REMARK 500 OD1 ASP A 56 HD22 ASN A 60 1.52 REMARK 500 O ALA A 359 HG1 THR A 360 1.57 REMARK 500 O ALA B 359 HG1 THR B 360 1.58 REMARK 500 NH2 ARG B 353 O GLY B 473 2.16 REMARK 500 NH2 ARG A 353 O GLY A 473 2.17 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 LEU B 17 -74.93 -115.85 REMARK 500 ASP B 25 75.54 64.48 REMARK 500 ASP B 46 80.26 -157.60 REMARK 500 HIS B 71 123.66 -172.28 REMARK 500 THR B 360 -4.47 70.67 REMARK 500 ARG B 364 -20.71 -141.64 REMARK 500 PRO B 464 37.57 -87.02 REMARK 500 LEU B 471 -103.32 -125.32 REMARK 500 GLN A 6 38.23 -76.79 REMARK 500 LEU A 17 -73.57 -106.35 REMARK 500 ASP A 25 78.79 64.54 REMARK 500 ARG A 42 148.54 -175.19 REMARK 500 ASP A 46 76.98 -154.25 REMARK 500 PHE A 59 4.97 -69.81 REMARK 500 HIS A 71 134.28 -174.26 REMARK 500 VAL A 173 -62.32 -106.32 REMARK 500 PRO A 233 46.15 -81.02 REMARK 500 ALA A 313 89.60 69.63 REMARK 500 PRO A 314 -138.00 -5.42 REMARK 500 ARG A 364 -18.31 -140.01 REMARK 500 ALA A 386 38.03 -82.69 REMARK 500 HIS A 452 50.84 -150.79 REMARK 500 PRO A 464 32.09 -85.31 REMARK 500 LEU A 471 -104.33 -119.46 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 B 788 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 763 DISTANCE = 6.17 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 FE B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 167 NE2 REMARK 620 2 HIS B 218 NE2 85.6 REMARK 620 3 HIS B 282 NE2 94.8 92.8 REMARK 620 4 HIS B 472 NE2 87.5 171.9 91.9 REMARK 620 5 HOH B 752 O 166.6 87.6 97.0 98.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 167 NE2 REMARK 620 2 HIS A 218 NE2 86.3 REMARK 620 3 HIS A 282 NE2 91.6 88.2 REMARK 620 4 HIS A 472 NE2 83.1 169.2 94.3 REMARK 620 5 HOH A 741 O 163.0 92.8 105.4 96.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 DBREF 6OJW B 2 481 UNP Q53353 LSDX1_SPHPI 2 481 DBREF 6OJW A 2 481 UNP Q53353 LSDX1_SPHPI 2 481 SEQRES 1 B 480 ALA HIS PHE PRO GLN THR PRO GLY PHE SER GLY THR LEU SEQRES 2 B 480 ARG PRO LEU ARG ILE GLU GLY ASP ILE LEU ASP ILE GLU SEQRES 3 B 480 ILE GLU GLY GLU VAL PRO PRO GLN LEU ASN GLY THR PHE SEQRES 4 B 480 HIS ARG VAL HIS PRO ASP ALA GLN PHE PRO PRO ARG PHE SEQRES 5 B 480 GLU ASP ASP GLN PHE PHE ASN GLY ASP GLY MET VAL SER SEQRES 6 B 480 LEU PHE ARG PHE HIS ASP GLY LYS ILE ASP PHE ARG GLN SEQRES 7 B 480 ARG TYR ALA GLN THR ASP LYS TRP LYS VAL GLU ARG LYS SEQRES 8 B 480 ALA GLY LYS SER LEU PHE GLY ALA TYR ARG ASN PRO LEU SEQRES 9 B 480 THR ASP ASP ALA SER VAL GLN GLY MET ILE ARG GLY THR SEQRES 10 B 480 ALA ASN THR ASN VAL MET VAL HIS ALA GLY LYS LEU TYR SEQRES 11 B 480 ALA MET LYS GLU ASP SER PRO CYS LEU ILE MET ASP PRO SEQRES 12 B 480 LEU THR LEU GLU THR GLU GLY TYR THR ASN PHE ASP GLY SEQRES 13 B 480 LYS LEU GLN SER GLN THR PHE CYS ALA HIS PRO LYS ILE SEQRES 14 B 480 ASP PRO VAL THR GLY ASN LEU CYS ALA PHE ALA TYR GLY SEQRES 15 B 480 ALA LYS GLY LEU MET THR LEU ASP MET ALA TYR ILE GLU SEQRES 16 B 480 ILE SER PRO THR GLY LYS LEU LEU LYS GLU ILE PRO PHE SEQRES 17 B 480 GLN ASN PRO TYR TYR CYS MET MET HIS ASP PHE GLY VAL SEQRES 18 B 480 THR GLU ASP TYR ALA VAL PHE ALA VAL MET PRO LEU LEU SEQRES 19 B 480 SER SER TRP ASP ARG LEU GLU GLN ARG LEU PRO PHE PHE SEQRES 20 B 480 GLY PHE ASP THR THR LEU PRO CYS TYR LEU GLY ILE LEU SEQRES 21 B 480 PRO ARG ASN GLY ASP ALA ARG ASP LEU ARG TRP PHE LYS SEQRES 22 B 480 THR GLY ASN CYS PHE VAL GLY HIS VAL MET ASN ALA PHE SEQRES 23 B 480 ASN ASP GLY THR LYS VAL HIS ILE ASP MET PRO VAL SER SEQRES 24 B 480 ARG ASN ASN SER PHE PRO PHE PHE ASP VAL HIS GLY ALA SEQRES 25 B 480 PRO PHE ASP PRO VAL ALA GLY GLN GLY PHE LEU THR ARG SEQRES 26 B 480 TRP THR VAL ASP MET ALA SER ASN GLY ASP SER PHE GLU SEQRES 27 B 480 LYS THR GLU ARG LEU PHE ASP ARG PRO ASP GLU PHE PRO SEQRES 28 B 480 ARG ILE ASP GLU ARG TYR ALA THR ARG ALA TYR ARG HIS SEQRES 29 B 480 GLY TRP MET LEU ILE LEU ASP THR GLU LYS PRO TYR GLU SEQRES 30 B 480 ALA PRO GLY GLY ALA PHE TYR ALA LEU THR ASN THR LEU SEQRES 31 B 480 GLY HIS ILE ASP LEU ALA THR GLY LYS SER SER SER TRP SEQRES 32 B 480 TRP ALA GLY PRO ARG CYS ALA ILE GLN GLU PRO CYS PHE SEQRES 33 B 480 ILE PRO ARG SER PRO ASP ALA PRO GLU GLY ASP GLY TYR SEQRES 34 B 480 VAL ILE ALA LEU VAL ASP ASP HIS VAL ALA ASN TYR SER SEQRES 35 B 480 ASP LEU ALA ILE PHE ASP ALA GLN HIS VAL ASP GLN GLY SEQRES 36 B 480 PRO ILE ALA ARG ALA LYS LEU PRO VAL ARG ILE ARG GLN SEQRES 37 B 480 GLY LEU HIS GLY ASN TRP ALA ASP ALA SER ARG LEU SEQRES 1 A 480 ALA HIS PHE PRO GLN THR PRO GLY PHE SER GLY THR LEU SEQRES 2 A 480 ARG PRO LEU ARG ILE GLU GLY ASP ILE LEU ASP ILE GLU SEQRES 3 A 480 ILE GLU GLY GLU VAL PRO PRO GLN LEU ASN GLY THR PHE SEQRES 4 A 480 HIS ARG VAL HIS PRO ASP ALA GLN PHE PRO PRO ARG PHE SEQRES 5 A 480 GLU ASP ASP GLN PHE PHE ASN GLY ASP GLY MET VAL SER SEQRES 6 A 480 LEU PHE ARG PHE HIS ASP GLY LYS ILE ASP PHE ARG GLN SEQRES 7 A 480 ARG TYR ALA GLN THR ASP LYS TRP LYS VAL GLU ARG LYS SEQRES 8 A 480 ALA GLY LYS SER LEU PHE GLY ALA TYR ARG ASN PRO LEU SEQRES 9 A 480 THR ASP ASP ALA SER VAL GLN GLY MET ILE ARG GLY THR SEQRES 10 A 480 ALA ASN THR ASN VAL MET VAL HIS ALA GLY LYS LEU TYR SEQRES 11 A 480 ALA MET LYS GLU ASP SER PRO CYS LEU ILE MET ASP PRO SEQRES 12 A 480 LEU THR LEU GLU THR GLU GLY TYR THR ASN PHE ASP GLY SEQRES 13 A 480 LYS LEU GLN SER GLN THR PHE CYS ALA HIS PRO LYS ILE SEQRES 14 A 480 ASP PRO VAL THR GLY ASN LEU CYS ALA PHE ALA TYR GLY SEQRES 15 A 480 ALA LYS GLY LEU MET THR LEU ASP MET ALA TYR ILE GLU SEQRES 16 A 480 ILE SER PRO THR GLY LYS LEU LEU LYS GLU ILE PRO PHE SEQRES 17 A 480 GLN ASN PRO TYR TYR CYS MET MET HIS ASP PHE GLY VAL SEQRES 18 A 480 THR GLU ASP TYR ALA VAL PHE ALA VAL MET PRO LEU LEU SEQRES 19 A 480 SER SER TRP ASP ARG LEU GLU GLN ARG LEU PRO PHE PHE SEQRES 20 A 480 GLY PHE ASP THR THR LEU PRO CYS TYR LEU GLY ILE LEU SEQRES 21 A 480 PRO ARG ASN GLY ASP ALA ARG ASP LEU ARG TRP PHE LYS SEQRES 22 A 480 THR GLY ASN CYS PHE VAL GLY HIS VAL MET ASN ALA PHE SEQRES 23 A 480 ASN ASP GLY THR LYS VAL HIS ILE ASP MET PRO VAL SER SEQRES 24 A 480 ARG ASN ASN SER PHE PRO PHE PHE ASP VAL HIS GLY ALA SEQRES 25 A 480 PRO PHE ASP PRO VAL ALA GLY GLN GLY PHE LEU THR ARG SEQRES 26 A 480 TRP THR VAL ASP MET ALA SER ASN GLY ASP SER PHE GLU SEQRES 27 A 480 LYS THR GLU ARG LEU PHE ASP ARG PRO ASP GLU PHE PRO SEQRES 28 A 480 ARG ILE ASP GLU ARG TYR ALA THR ARG ALA TYR ARG HIS SEQRES 29 A 480 GLY TRP MET LEU ILE LEU ASP THR GLU LYS PRO TYR GLU SEQRES 30 A 480 ALA PRO GLY GLY ALA PHE TYR ALA LEU THR ASN THR LEU SEQRES 31 A 480 GLY HIS ILE ASP LEU ALA THR GLY LYS SER SER SER TRP SEQRES 32 A 480 TRP ALA GLY PRO ARG CYS ALA ILE GLN GLU PRO CYS PHE SEQRES 33 A 480 ILE PRO ARG SER PRO ASP ALA PRO GLU GLY ASP GLY TYR SEQRES 34 A 480 VAL ILE ALA LEU VAL ASP ASP HIS VAL ALA ASN TYR SER SEQRES 35 A 480 ASP LEU ALA ILE PHE ASP ALA GLN HIS VAL ASP GLN GLY SEQRES 36 A 480 PRO ILE ALA ARG ALA LYS LEU PRO VAL ARG ILE ARG GLN SEQRES 37 A 480 GLY LEU HIS GLY ASN TRP ALA ASP ALA SER ARG LEU HET FE B 501 1 HET GOL B 502 14 HET GOL B 503 14 HET FE A 501 1 HET MG A 502 1 HET GOL A 503 14 HETNAM FE FE (III) ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FE 2(FE 3+) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 MG MG 2+ FORMUL 9 HOH *351(H2 O) HELIX 1 AA1 THR B 7 ARG B 15 5 9 HELIX 2 AA2 GLN B 57 GLY B 61 5 5 HELIX 3 AA3 THR B 84 GLY B 94 1 11 HELIX 4 AA4 ASN B 103 ASP B 107 5 5 HELIX 5 AA5 ASP B 108 GLN B 112 5 5 HELIX 6 AA6 SER B 237 GLN B 243 1 7 HELIX 7 AA7 ASP B 266 LEU B 270 5 5 HELIX 8 AA8 GLU B 356 ALA B 359 5 4 HELIX 9 AA9 HIS B 452 GLY B 456 5 5 HELIX 10 AB1 SER B 479 LEU B 481 5 3 HELIX 11 AB2 THR A 7 ARG A 15 5 9 HELIX 12 AB3 GLN A 57 GLY A 61 5 5 HELIX 13 AB4 THR A 84 GLY A 94 1 11 HELIX 14 AB5 ASN A 103 ASP A 107 5 5 HELIX 15 AB6 ASP A 108 GLN A 112 5 5 HELIX 16 AB7 SER A 237 GLN A 243 1 7 HELIX 17 AB8 ASP A 266 LEU A 270 5 5 HELIX 18 AB9 GLU A 356 ALA A 359 5 4 HELIX 19 AC1 HIS A 452 GLY A 456 5 5 HELIX 20 AC2 SER A 479 LEU A 481 5 3 SHEET 1 AA110 GLY B 473 ASP B 477 0 SHEET 2 AA110 GLY B 38 PRO B 45 -1 N THR B 39 O ALA B 476 SHEET 3 AA110 GLY B 63 HIS B 71 -1 O SER B 66 N ARG B 42 SHEET 4 AA110 LYS B 74 TYR B 81 -1 O ARG B 78 N LEU B 67 SHEET 5 AA110 GLU B 20 ILE B 23 -1 N ILE B 23 O PHE B 77 SHEET 6 AA110 GLU A 20 ILE A 23 -1 O ASP A 22 N GLU B 20 SHEET 7 AA110 LYS A 74 TYR A 81 -1 O PHE A 77 N ILE A 23 SHEET 8 AA110 GLY A 63 HIS A 71 -1 N LEU A 67 O ARG A 78 SHEET 9 AA110 GLY A 38 PRO A 45 -1 N ARG A 42 O SER A 66 SHEET 10 AA110 GLY A 473 ASP A 477 -1 O ALA A 476 N THR A 39 SHEET 1 AA2 5 GLU B 27 GLY B 30 0 SHEET 2 AA2 5 ALA B 459 LYS B 462 -1 O ARG B 460 N GLU B 29 SHEET 3 AA2 5 TYR B 442 ASP B 449 -1 N ILE B 447 O ALA B 459 SHEET 4 AA2 5 GLY B 429 ASP B 437 -1 N ASP B 437 O TYR B 442 SHEET 5 AA2 5 CYS B 410 ILE B 412 -1 N ALA B 411 O ASP B 436 SHEET 1 AA3 5 GLU B 27 GLY B 30 0 SHEET 2 AA3 5 ALA B 459 LYS B 462 -1 O ARG B 460 N GLU B 29 SHEET 3 AA3 5 TYR B 442 ASP B 449 -1 N ILE B 447 O ALA B 459 SHEET 4 AA3 5 GLY B 429 ASP B 437 -1 N ASP B 437 O TYR B 442 SHEET 5 AA3 5 CYS B 416 PRO B 419 -1 N ILE B 418 O TYR B 430 SHEET 1 AA4 4 ASN B 122 HIS B 126 0 SHEET 2 AA4 4 LYS B 129 MET B 133 -1 O TYR B 131 N MET B 124 SHEET 3 AA4 4 CYS B 139 MET B 142 -1 O LEU B 140 N ALA B 132 SHEET 4 AA4 4 THR B 149 THR B 153 -1 O GLU B 150 N ILE B 141 SHEET 1 AA5 4 LYS B 169 ILE B 170 0 SHEET 2 AA5 4 LEU B 177 TYR B 182 -1 O CYS B 178 N LYS B 169 SHEET 3 AA5 4 ASP B 191 ILE B 197 -1 O ILE B 195 N ALA B 179 SHEET 4 AA5 4 LEU B 203 GLN B 210 -1 O PHE B 209 N MET B 192 SHEET 1 AA6 4 GLY B 221 VAL B 222 0 SHEET 2 AA6 4 TYR B 226 VAL B 231 -1 O VAL B 228 N GLY B 221 SHEET 3 AA6 4 CYS B 256 PRO B 262 -1 O TYR B 257 N VAL B 231 SHEET 4 AA6 4 ARG B 271 THR B 275 -1 O PHE B 273 N LEU B 258 SHEET 1 AA7 2 LEU B 234 LEU B 235 0 SHEET 2 AA7 2 GLY B 249 PHE B 250 -1 O GLY B 249 N LEU B 235 SHEET 1 AA8 3 PHE B 279 VAL B 280 0 SHEET 2 AA8 3 LYS B 292 SER B 300 -1 O SER B 300 N PHE B 279 SHEET 3 AA8 3 ASN B 285 ASP B 289 -1 N PHE B 287 O HIS B 294 SHEET 1 AA9 4 PHE B 279 VAL B 280 0 SHEET 2 AA9 4 LYS B 292 SER B 300 -1 O SER B 300 N PHE B 279 SHEET 3 AA9 4 PHE B 323 ASP B 330 -1 O VAL B 329 N VAL B 293 SHEET 4 AA9 4 LYS B 340 ARG B 343 -1 O GLU B 342 N ARG B 326 SHEET 1 AB1 4 ASP B 349 ILE B 354 0 SHEET 2 AB1 4 HIS B 365 ILE B 370 -1 O TRP B 367 N ARG B 353 SHEET 3 AB1 4 THR B 390 ASP B 395 -1 O GLY B 392 N MET B 368 SHEET 4 AB1 4 SER B 401 TRP B 405 -1 O SER B 402 N HIS B 393 SHEET 1 AB2 5 GLU A 27 GLY A 30 0 SHEET 2 AB2 5 ALA A 459 LEU A 463 -1 O ARG A 460 N GLU A 29 SHEET 3 AB2 5 TYR A 442 ASP A 449 -1 N ILE A 447 O ALA A 459 SHEET 4 AB2 5 GLY A 429 ASP A 437 -1 N VAL A 431 O PHE A 448 SHEET 5 AB2 5 CYS A 410 ILE A 412 -1 N ALA A 411 O ASP A 436 SHEET 1 AB3 5 GLU A 27 GLY A 30 0 SHEET 2 AB3 5 ALA A 459 LEU A 463 -1 O ARG A 460 N GLU A 29 SHEET 3 AB3 5 TYR A 442 ASP A 449 -1 N ILE A 447 O ALA A 459 SHEET 4 AB3 5 GLY A 429 ASP A 437 -1 N VAL A 431 O PHE A 448 SHEET 5 AB3 5 CYS A 416 PRO A 419 -1 N ILE A 418 O TYR A 430 SHEET 1 AB4 4 ASN A 122 HIS A 126 0 SHEET 2 AB4 4 LYS A 129 MET A 133 -1 O TYR A 131 N MET A 124 SHEET 3 AB4 4 LEU A 140 MET A 142 -1 O LEU A 140 N ALA A 132 SHEET 4 AB4 4 THR A 149 TYR A 152 -1 O GLU A 150 N ILE A 141 SHEET 1 AB5 4 LYS A 169 ILE A 170 0 SHEET 2 AB5 4 LEU A 177 TYR A 182 -1 O CYS A 178 N LYS A 169 SHEET 3 AB5 4 ASP A 191 ILE A 197 -1 O ILE A 197 N LEU A 177 SHEET 4 AB5 4 LEU A 203 GLN A 210 -1 O PHE A 209 N MET A 192 SHEET 1 AB6 4 GLY A 221 VAL A 222 0 SHEET 2 AB6 4 TYR A 226 VAL A 231 -1 O VAL A 228 N GLY A 221 SHEET 3 AB6 4 CYS A 256 PRO A 262 -1 O GLY A 259 N PHE A 229 SHEET 4 AB6 4 ARG A 271 THR A 275 -1 O THR A 275 N CYS A 256 SHEET 1 AB7 2 LEU A 234 SER A 236 0 SHEET 2 AB7 2 PHE A 248 PHE A 250 -1 O GLY A 249 N LEU A 235 SHEET 1 AB8 3 PHE A 279 VAL A 280 0 SHEET 2 AB8 3 LYS A 292 SER A 300 -1 O SER A 300 N PHE A 279 SHEET 3 AB8 3 ASN A 285 ASP A 289 -1 N ASP A 289 O LYS A 292 SHEET 1 AB9 4 PHE A 279 VAL A 280 0 SHEET 2 AB9 4 LYS A 292 SER A 300 -1 O SER A 300 N PHE A 279 SHEET 3 AB9 4 PHE A 323 ASP A 330 -1 O VAL A 329 N VAL A 293 SHEET 4 AB9 4 LYS A 340 ARG A 343 -1 O GLU A 342 N ARG A 326 SHEET 1 AC1 4 ASP A 349 ILE A 354 0 SHEET 2 AC1 4 HIS A 365 ILE A 370 -1 O TRP A 367 N ARG A 353 SHEET 3 AC1 4 THR A 390 ASP A 395 -1 O GLY A 392 N MET A 368 SHEET 4 AC1 4 SER A 401 TRP A 405 -1 O SER A 402 N HIS A 393 LINK NE2 HIS B 167 FE FE B 501 1555 1555 2.25 LINK NE2 HIS B 218 FE FE B 501 1555 1555 1.95 LINK NE2 HIS B 282 FE FE B 501 1555 1555 2.17 LINK NE2 HIS B 472 FE FE B 501 1555 1555 2.10 LINK FE FE B 501 O HOH B 752 1555 1555 2.48 LINK NE2 HIS A 167 FE FE A 501 1555 1555 2.36 LINK NE2 HIS A 218 FE FE A 501 1555 1555 1.96 LINK NE2 HIS A 282 FE FE A 501 1555 1555 2.15 LINK O LEU A 463 MG MG A 502 1555 1555 2.74 LINK NE2 HIS A 472 FE FE A 501 1555 1555 2.09 LINK FE FE A 501 O HOH A 741 1555 1555 2.53 SITE 1 AC1 5 HIS B 167 HIS B 218 HIS B 282 HIS B 472 SITE 2 AC1 5 HOH B 752 SITE 1 AC2 3 ALA B 127 TYR B 131 THR B 153 SITE 1 AC3 5 ASP A 423 ASP B 85 GLU B 150 GLY B 151 SITE 2 AC3 5 TYR B 152 SITE 1 AC4 5 HIS A 167 HIS A 218 HIS A 282 HIS A 472 SITE 2 AC4 5 HOH A 741 SITE 1 AC5 5 TYR A 442 ASP A 444 LYS A 462 LEU A 463 SITE 2 AC5 5 ARG B 15 SITE 1 AC6 5 ALA A 127 TYR A 131 THR A 153 PHE A 155 SITE 2 AC6 5 GLY A 201 CRYST1 183.259 183.259 95.081 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 0.005457 0.003150 0.000000 0.00000 SCALE2 0.000000 0.006301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010517 0.00000