HEADER METAL TRANSPORT 23-JUL-21 7FFU TITLE OSMIUM-BOUND HUMAN SERUM TRANSFERRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEROTRANSFERRIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSFERRIN,BETA-1 METAL-BINDING GLOBULIN,SIDEROPHILIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS OSMIUM, TRANFERRIN, IRON TRANSPORT, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.WANG,H.SUN REVDAT 2 29-NOV-23 7FFU 1 REMARK REVDAT 1 22-JUN-22 7FFU 0 JRNL AUTH M.WANG,H.WANG,X.XU,T.P.LAI,Y.ZHOU,Q.HAO,H.LI,H.SUN JRNL TITL BINDING OF RUTHENIUM AND OSMIUM AT NON‐IRON SITES OF JRNL TITL 2 TRANSFERRIN ACCOUNTS FOR THEIR IRON-INDEPENDENT CELLULAR JRNL TITL 3 UPTAKE. JRNL REF J.INORG.BIOCHEM. V. 234 11885 2022 JRNL REFN ISSN 0162-0134 JRNL PMID 35690040 JRNL DOI 10.1016/J.JINORGBIO.2022.111885 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260:000 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) : 48.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 35513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.290 REMARK 3 FREE R VALUE TEST SET COUNT : 1878 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 48.8520 - 6.1132 0.99 2755 158 0.2025 0.2265 REMARK 3 2 6.1132 - 4.8537 1.00 2652 161 0.1931 0.2187 REMARK 3 3 4.8537 - 4.2405 1.00 2638 158 0.1568 0.1897 REMARK 3 4 4.2405 - 3.8530 1.00 2612 140 0.1686 0.1974 REMARK 3 5 3.8530 - 3.5769 1.00 2618 154 0.1874 0.1906 REMARK 3 6 3.5769 - 3.3661 1.00 2592 152 0.1939 0.2436 REMARK 3 7 3.3661 - 3.1975 1.00 2636 137 0.2050 0.2387 REMARK 3 8 3.1975 - 3.0584 1.00 2602 128 0.2195 0.2801 REMARK 3 9 3.0584 - 2.9406 1.00 2606 153 0.2286 0.2886 REMARK 3 10 2.9406 - 2.8392 1.00 2617 120 0.2310 0.2540 REMARK 3 11 2.8392 - 2.7504 1.00 2562 154 0.2263 0.2604 REMARK 3 12 2.7504 - 2.6718 0.98 2542 137 0.2428 0.2722 REMARK 3 13 2.6718 - 2.6015 0.85 2203 126 0.2521 0.3100 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) : 22.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.24 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0068 6.5043 -17.7094 REMARK 3 T TENSOR REMARK 3 T11: 0.3529 T22: 0.4730 REMARK 3 T33: 0.0847 T12: 0.0737 REMARK 3 T13: -0.0124 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 2.3486 L22: 1.5003 REMARK 3 L33: 3.1317 L12: 0.2430 REMARK 3 L13: 0.3595 L23: 0.4251 REMARK 3 S TENSOR REMARK 3 S11: 0.0044 S12: 0.4150 S13: 0.1507 REMARK 3 S21: -0.3193 S22: -0.0610 S23: 0.0501 REMARK 3 S31: -0.0926 S32: 0.0115 S33: 0.0182 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 259 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.3227 17.8089 12.2955 REMARK 3 T TENSOR REMARK 3 T11: 0.3842 T22: 0.5318 REMARK 3 T33: 0.0754 T12: -0.0753 REMARK 3 T13: 0.0650 T23: -0.0518 REMARK 3 L TENSOR REMARK 3 L11: 0.4246 L22: 0.7194 REMARK 3 L33: 1.5538 L12: 0.0740 REMARK 3 L13: 0.0179 L23: 0.1918 REMARK 3 S TENSOR REMARK 3 S11: 0.1321 S12: -0.0816 S13: 0.1001 REMARK 3 S21: 0.1330 S22: -0.1349 S23: 0.0890 REMARK 3 S31: -0.2234 S32: -0.0976 S33: -0.0342 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 260 THROUGH 294 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0355 14.8103 -15.5641 REMARK 3 T TENSOR REMARK 3 T11: 0.4674 T22: 0.4078 REMARK 3 T33: 0.1484 T12: 0.1247 REMARK 3 T13: -0.0240 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 6.5543 L22: 4.5174 REMARK 3 L33: 6.6368 L12: 1.0765 REMARK 3 L13: 0.6157 L23: -0.0060 REMARK 3 S TENSOR REMARK 3 S11: -0.2903 S12: 0.2210 S13: 0.1688 REMARK 3 S21: -0.3178 S22: 0.0365 S23: 0.5440 REMARK 3 S31: -0.2732 S32: -0.6027 S33: 0.2186 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 295 THROUGH 447 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.2881 34.7218 -1.9116 REMARK 3 T TENSOR REMARK 3 T11: 0.5721 T22: 0.6811 REMARK 3 T33: 0.2436 T12: -0.2135 REMARK 3 T13: 0.0725 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 0.7210 L22: 1.8992 REMARK 3 L33: 1.2128 L12: 0.7536 REMARK 3 L13: -0.6464 L23: -0.8838 REMARK 3 S TENSOR REMARK 3 S11: 0.2184 S12: -0.1142 S13: 0.1335 REMARK 3 S21: 0.2746 S22: -0.2987 S23: -0.3525 REMARK 3 S31: -0.5066 S32: 0.6118 S33: 0.1044 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 448 THROUGH 590 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.7508 53.7983 -13.6183 REMARK 3 T TENSOR REMARK 3 T11: 0.7597 T22: 0.5769 REMARK 3 T33: 0.2578 T12: -0.2214 REMARK 3 T13: 0.0877 T23: 0.0327 REMARK 3 L TENSOR REMARK 3 L11: 1.6891 L22: 1.6140 REMARK 3 L33: 2.9982 L12: 0.6689 REMARK 3 L13: -1.5736 L23: -2.0034 REMARK 3 S TENSOR REMARK 3 S11: 0.2846 S12: -0.0629 S13: 0.3094 REMARK 3 S21: 0.5446 S22: -0.0724 S23: 0.3178 REMARK 3 S31: -0.4089 S32: -0.1474 S33: -0.2478 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 591 THROUGH 679 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.3551 41.2457 3.0120 REMARK 3 T TENSOR REMARK 3 T11: 0.9326 T22: 0.8774 REMARK 3 T33: 0.3889 T12: -0.3838 REMARK 3 T13: 0.1075 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 3.0724 L22: 2.1553 REMARK 3 L33: 1.2869 L12: 0.4809 REMARK 3 L13: 0.1696 L23: -0.7700 REMARK 3 S TENSOR REMARK 3 S11: 0.2863 S12: -0.2208 S13: 0.4692 REMARK 3 S21: 0.6178 S22: -0.2269 S23: -0.1697 REMARK 3 S31: -0.6688 S32: 0.5079 S33: -0.0233 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 7FFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.14026 REMARK 200 MONOCHROMATOR : GRAPHITE MONOCHROMER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 1.0 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35884 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.80 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 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) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.00 REMARK 200 R MERGE FOR SHELL (I) : 0.85000 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 REMARK 200 STARTING MODEL: 4X1B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PIPES-NAOH 0.1M PH 6.6, DISODIUM REMARK 280 MALONATE 8MM, GLYCEROL 18%, PEG 3350 17%, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 53.65650 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 53.65650 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 68.91550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 78.36450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 68.91550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 78.36450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.65650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 68.91550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 78.36450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.65650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 68.91550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 78.36450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 VAL A 1 REMARK 465 PRO A 2 REMARK 465 GLU A 333 REMARK 465 ALA A 334 REMARK 465 PRO A 335 REMARK 465 THR A 336 REMARK 465 ASP A 337 REMARK 465 GLU A 338 REMARK 465 LYS A 414 REMARK 465 SER A 415 REMARK 465 ASP A 416 REMARK 465 ASN A 417 REMARK 465 CYS A 418 REMARK 465 GLU A 419 REMARK 465 ASP A 420 REMARK 465 THR A 421 REMARK 465 PRO A 422 REMARK 465 GLU A 423 REMARK 465 VAL A 612 REMARK 465 THR A 613 REMARK 465 ASP A 614 REMARK 465 CYS A 615 REMARK 465 SER A 616 REMARK 465 GLY A 617 REMARK 465 ASN A 618 REMARK 465 PHE A 619 REMARK 465 CYS A 620 REMARK 465 LEU A 621 REMARK 465 PHE A 622 REMARK 465 ARG A 623 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 LYS A 88 CG CD CE NZ REMARK 470 GLU A 89 CG CD OE1 OE2 REMARK 470 GLU A 272 CG CD OE1 OE2 REMARK 470 LYS A 340 CG CD CE NZ REMARK 470 HIS A 349 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 350 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 363 CG1 CG2 REMARK 470 LYS A 365 CG CD CE NZ REMARK 470 TYR A 412 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 602 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 603 CG CD OE1 NE2 REMARK 470 HIS A 606 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 611 CG OD1 ND2 REMARK 470 GLU A 625 CG CD OE1 OE2 REMARK 470 LYS A 640 CG CD CE NZ REMARK 470 ARG A 644 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 653 CG CD OE1 OE2 REMARK 470 GLU A 654 CG CD OE1 OE2 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 LYS A 4 58.40 -108.62 REMARK 500 VAL A 80 -32.87 -133.75 REMARK 500 TRP A 128 -62.18 -145.27 REMARK 500 CYS A 179 33.38 -94.79 REMARK 500 CYS A 241 75.08 -163.19 REMARK 500 SER A 287 138.02 -170.13 REMARK 500 LEU A 294 -45.80 70.18 REMARK 500 LYS A 340 161.82 76.40 REMARK 500 SER A 362 1.01 -69.99 REMARK 500 TRP A 460 -58.91 -140.49 REMARK 500 LYS A 527 -34.72 -134.22 REMARK 500 VAL A 533 -156.61 -142.11 REMARK 500 GLU A 573 35.78 -92.06 REMARK 500 CYS A 577 63.62 -156.63 REMARK 500 THR A 626 -107.65 -77.08 REMARK 500 LEU A 630 -56.09 69.87 REMARK 500 HIS A 642 -122.75 61.98 REMARK 500 ARG A 644 49.79 -76.96 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 OS A 703 OS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 14 NE2 REMARK 620 2 HIS A 289 NE2 94.9 REMARK 620 3 HOH A 801 O 115.8 69.8 REMARK 620 4 HOH A 803 O 77.1 102.9 165.1 REMARK 620 5 HOH A 809 O 167.4 79.9 73.3 92.8 REMARK 620 6 HOH A 827 O 114.0 149.6 88.3 93.1 73.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 701 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 392 OD1 REMARK 620 2 TYR A 426 OH 96.3 REMARK 620 3 TYR A 517 OH 165.0 91.0 REMARK 620 4 HIS A 585 NE2 95.2 111.0 94.4 REMARK 620 5 MLI A 702 O7 82.2 89.5 84.8 159.5 REMARK 620 6 MLI A 702 O9 89.7 166.7 80.6 80.1 79.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OS A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WTD RELATED DB: PDB REMARK 900 RUTHENIUM-ANALOGUE DBREF 7FFU A 1 679 UNP P02787 TRFE_HUMAN 20 698 SEQADV 7FFU VAL A 429 UNP P02787 ILE 448 VARIANT SEQRES 1 A 679 VAL PRO ASP LYS THR VAL ARG TRP CYS ALA VAL SER GLU SEQRES 2 A 679 HIS GLU ALA THR LYS CYS GLN SER PHE ARG ASP HIS MET SEQRES 3 A 679 LYS SER VAL ILE PRO SER ASP GLY PRO SER VAL ALA CYS SEQRES 4 A 679 VAL LYS LYS ALA SER TYR LEU ASP CYS ILE ARG ALA ILE SEQRES 5 A 679 ALA ALA ASN GLU ALA ASP ALA VAL THR LEU ASP ALA GLY SEQRES 6 A 679 LEU VAL TYR ASP ALA TYR LEU ALA PRO ASN ASN LEU LYS SEQRES 7 A 679 PRO VAL VAL ALA GLU PHE TYR GLY SER LYS GLU ASP PRO SEQRES 8 A 679 GLN THR PHE TYR TYR ALA VAL ALA VAL VAL LYS LYS ASP SEQRES 9 A 679 SER GLY PHE GLN MET ASN GLN LEU ARG GLY LYS LYS SER SEQRES 10 A 679 CYS HIS THR GLY LEU GLY ARG SER ALA GLY TRP ASN ILE SEQRES 11 A 679 PRO ILE GLY LEU LEU TYR CYS ASP LEU PRO GLU PRO ARG SEQRES 12 A 679 LYS PRO LEU GLU LYS ALA VAL ALA ASN PHE PHE SER GLY SEQRES 13 A 679 SER CYS ALA PRO CYS ALA ASP GLY THR ASP PHE PRO GLN SEQRES 14 A 679 LEU CYS GLN LEU CYS PRO GLY CYS GLY CYS SER THR LEU SEQRES 15 A 679 ASN GLN TYR PHE GLY TYR SER GLY ALA PHE LYS CYS LEU SEQRES 16 A 679 LYS ASP GLY ALA GLY ASP VAL ALA PHE VAL LYS HIS SER SEQRES 17 A 679 THR ILE PHE GLU ASN LEU ALA ASN LYS ALA ASP ARG ASP SEQRES 18 A 679 GLN TYR GLU LEU LEU CYS LEU ASP ASN THR ARG LYS PRO SEQRES 19 A 679 VAL ASP GLU TYR LYS ASP CYS HIS LEU ALA GLN VAL PRO SEQRES 20 A 679 SER HIS THR VAL VAL ALA ARG SER MET GLY GLY LYS GLU SEQRES 21 A 679 ASP LEU ILE TRP GLU LEU LEU ASN GLN ALA GLN GLU HIS SEQRES 22 A 679 PHE GLY LYS ASP LYS SER LYS GLU PHE GLN LEU PHE SER SEQRES 23 A 679 SER PRO HIS GLY LYS ASP LEU LEU PHE LYS ASP SER ALA SEQRES 24 A 679 HIS GLY PHE LEU LYS VAL PRO PRO ARG MET ASP ALA LYS SEQRES 25 A 679 MET TYR LEU GLY TYR GLU TYR VAL THR ALA ILE ARG ASN SEQRES 26 A 679 LEU ARG GLU GLY THR CYS PRO GLU ALA PRO THR ASP GLU SEQRES 27 A 679 CYS LYS PRO VAL LYS TRP CYS ALA LEU SER HIS HIS GLU SEQRES 28 A 679 ARG LEU LYS CYS ASP GLU TRP SER VAL ASN SER VAL GLY SEQRES 29 A 679 LYS ILE GLU CYS VAL SER ALA GLU THR THR GLU ASP CYS SEQRES 30 A 679 ILE ALA LYS ILE MET ASN GLY GLU ALA ASP ALA MET SER SEQRES 31 A 679 LEU ASP GLY GLY PHE VAL TYR ILE ALA GLY LYS CYS GLY SEQRES 32 A 679 LEU VAL PRO VAL LEU ALA GLU ASN TYR ASN LYS SER ASP SEQRES 33 A 679 ASN CYS GLU ASP THR PRO GLU ALA GLY TYR PHE ALA VAL SEQRES 34 A 679 ALA VAL VAL LYS LYS SER ALA SER ASP LEU THR TRP ASP SEQRES 35 A 679 ASN LEU LYS GLY LYS LYS SER CYS HIS THR ALA VAL GLY SEQRES 36 A 679 ARG THR ALA GLY TRP ASN ILE PRO MET GLY LEU LEU TYR SEQRES 37 A 679 ASN LYS ILE ASN HIS CYS ARG PHE ASP GLU PHE PHE SER SEQRES 38 A 679 GLU GLY CYS ALA PRO GLY SER LYS LYS ASP SER SER LEU SEQRES 39 A 679 CYS LYS LEU CYS MET GLY SER GLY LEU ASN LEU CYS GLU SEQRES 40 A 679 PRO ASN ASN LYS GLU GLY TYR TYR GLY TYR THR GLY ALA SEQRES 41 A 679 PHE ARG CYS LEU VAL GLU LYS GLY ASP VAL ALA PHE VAL SEQRES 42 A 679 LYS HIS GLN THR VAL PRO GLN ASN THR GLY GLY LYS ASN SEQRES 43 A 679 PRO ASP PRO TRP ALA LYS ASN LEU ASN GLU LYS ASP TYR SEQRES 44 A 679 GLU LEU LEU CYS LEU ASP GLY THR ARG LYS PRO VAL GLU SEQRES 45 A 679 GLU TYR ALA ASN CYS HIS LEU ALA ARG ALA PRO ASN HIS SEQRES 46 A 679 ALA VAL VAL THR ARG LYS ASP LYS GLU ALA CYS VAL HIS SEQRES 47 A 679 LYS ILE LEU ARG GLN GLN GLN HIS LEU PHE GLY SER ASN SEQRES 48 A 679 VAL THR ASP CYS SER GLY ASN PHE CYS LEU PHE ARG SER SEQRES 49 A 679 GLU THR LYS ASP LEU LEU PHE ARG ASP ASP THR VAL CYS SEQRES 50 A 679 LEU ALA LYS LEU HIS ASP ARG ASN THR TYR GLU LYS TYR SEQRES 51 A 679 LEU GLY GLU GLU TYR VAL LYS ALA VAL GLY ASN LEU ARG SEQRES 52 A 679 LYS CYS SER THR SER SER LEU LEU GLU ALA CYS THR PHE SEQRES 53 A 679 ARG ARG PRO HET FE A 701 1 HET MLI A 702 7 HET OS A 703 1 HETNAM FE FE (III) ION HETNAM MLI MALONATE ION HETNAM OS OSMIUM ION FORMUL 2 FE FE 3+ FORMUL 3 MLI C3 H2 O4 2- FORMUL 4 OS OS 3+ FORMUL 5 HOH *28(H2 O) HELIX 1 AA1 SER A 12 SER A 28 1 17 HELIX 2 AA2 SER A 44 ALA A 54 1 11 HELIX 3 AA3 ASP A 63 LEU A 72 1 10 HELIX 4 AA4 GLN A 108 LEU A 112 5 5 HELIX 5 AA5 TRP A 128 LEU A 135 1 8 HELIX 6 AA6 TYR A 136 LEU A 139 5 4 HELIX 7 AA7 PRO A 145 ASN A 152 1 8 HELIX 8 AA8 PHE A 167 GLN A 172 5 6 HELIX 9 AA9 PHE A 186 ASP A 197 1 12 HELIX 10 AB1 SER A 208 LEU A 214 1 7 HELIX 11 AB2 ASN A 216 ASP A 221 1 6 HELIX 12 AB3 ASP A 236 CYS A 241 5 6 HELIX 13 AB4 LYS A 259 GLY A 275 1 17 HELIX 14 AB5 ASP A 310 GLY A 316 1 7 HELIX 15 AB6 GLY A 316 GLY A 329 1 14 HELIX 16 AB7 SER A 348 SER A 362 1 15 HELIX 17 AB8 THR A 373 ASN A 383 1 11 HELIX 18 AB9 ASP A 392 CYS A 402 1 11 HELIX 19 AC1 TRP A 460 ASN A 472 1 13 HELIX 20 AC2 SER A 492 LYS A 496 5 5 HELIX 21 AC3 SER A 501 LEU A 505 5 5 HELIX 22 AC4 GLY A 516 LYS A 527 1 12 HELIX 23 AC5 GLN A 536 ASN A 541 1 6 HELIX 24 AC6 ASN A 555 LYS A 557 5 3 HELIX 25 AC7 GLU A 573 CYS A 577 5 5 HELIX 26 AC8 ARG A 590 ASP A 592 5 3 HELIX 27 AC9 LYS A 593 GLY A 609 1 17 HELIX 28 AD1 THR A 646 GLY A 652 1 7 HELIX 29 AD2 GLY A 652 ARG A 663 1 12 HELIX 30 AD3 LYS A 664 SER A 666 5 3 HELIX 31 AD4 SER A 668 ARG A 678 1 11 SHEET 1 AA1 2 THR A 5 ALA A 10 0 SHEET 2 AA1 2 SER A 36 LYS A 41 1 O ALA A 38 N TRP A 8 SHEET 1 AA2 4 VAL A 60 LEU A 62 0 SHEET 2 AA2 4 THR A 250 ARG A 254 -1 O THR A 250 N LEU A 62 SHEET 3 AA2 4 LEU A 77 GLY A 86 -1 N VAL A 81 O VAL A 251 SHEET 4 AA2 4 PRO A 91 GLN A 92 -1 O GLN A 92 N TYR A 85 SHEET 1 AA3 4 VAL A 60 LEU A 62 0 SHEET 2 AA3 4 THR A 250 ARG A 254 -1 O THR A 250 N LEU A 62 SHEET 3 AA3 4 LEU A 77 GLY A 86 -1 N VAL A 81 O VAL A 251 SHEET 4 AA3 4 GLY A 301 LYS A 304 -1 O LEU A 303 N ALA A 82 SHEET 1 AA4 6 GLY A 156 CYS A 158 0 SHEET 2 AA4 6 LYS A 116 HIS A 119 1 N HIS A 119 O CYS A 158 SHEET 3 AA4 6 VAL A 202 LYS A 206 1 O VAL A 202 N CYS A 118 SHEET 4 AA4 6 PHE A 94 LYS A 102 -1 N VAL A 98 O VAL A 205 SHEET 5 AA4 6 TYR A 223 LEU A 226 -1 O GLU A 224 N VAL A 101 SHEET 6 AA4 6 ARG A 232 PRO A 234 -1 O LYS A 233 N LEU A 225 SHEET 1 AA5 5 GLY A 156 CYS A 158 0 SHEET 2 AA5 5 LYS A 116 HIS A 119 1 N HIS A 119 O CYS A 158 SHEET 3 AA5 5 VAL A 202 LYS A 206 1 O VAL A 202 N CYS A 118 SHEET 4 AA5 5 PHE A 94 LYS A 102 -1 N VAL A 98 O VAL A 205 SHEET 5 AA5 5 ALA A 244 PRO A 247 -1 O VAL A 246 N TYR A 95 SHEET 1 AA6 2 VAL A 342 ALA A 346 0 SHEET 2 AA6 2 ILE A 366 SER A 370 1 O GLU A 367 N TRP A 344 SHEET 1 AA7 4 MET A 389 LEU A 391 0 SHEET 2 AA7 4 ALA A 586 THR A 589 -1 O ALA A 586 N LEU A 391 SHEET 3 AA7 4 VAL A 405 ASN A 411 -1 N LEU A 408 O VAL A 587 SHEET 4 AA7 4 CYS A 637 ALA A 639 -1 O ALA A 639 N ALA A 409 SHEET 1 AA8 6 GLU A 482 CYS A 484 0 SHEET 2 AA8 6 LYS A 448 HIS A 451 1 N HIS A 451 O CYS A 484 SHEET 3 AA8 6 VAL A 530 LYS A 534 1 O PHE A 532 N CYS A 450 SHEET 4 AA8 6 PHE A 427 LYS A 433 -1 N VAL A 431 O ALA A 531 SHEET 5 AA8 6 TYR A 559 LEU A 562 -1 O GLU A 560 N VAL A 432 SHEET 6 AA8 6 ARG A 568 PRO A 570 -1 O LYS A 569 N LEU A 561 SHEET 1 AA9 5 GLU A 482 CYS A 484 0 SHEET 2 AA9 5 LYS A 448 HIS A 451 1 N HIS A 451 O CYS A 484 SHEET 3 AA9 5 VAL A 530 LYS A 534 1 O PHE A 532 N CYS A 450 SHEET 4 AA9 5 PHE A 427 LYS A 433 -1 N VAL A 431 O ALA A 531 SHEET 5 AA9 5 ALA A 580 ARG A 581 -1 O ALA A 580 N ALA A 428 SSBOND 1 CYS A 9 CYS A 48 1555 1555 2.03 SSBOND 2 CYS A 19 CYS A 39 1555 1555 2.03 SSBOND 3 CYS A 118 CYS A 194 1555 1555 2.04 SSBOND 4 CYS A 137 CYS A 331 1555 1555 2.04 SSBOND 5 CYS A 158 CYS A 174 1555 1555 2.03 SSBOND 6 CYS A 161 CYS A 179 1555 1555 2.03 SSBOND 7 CYS A 171 CYS A 177 1555 1555 2.04 SSBOND 8 CYS A 227 CYS A 241 1555 1555 2.04 SSBOND 9 CYS A 339 CYS A 596 1555 1555 2.17 SSBOND 10 CYS A 345 CYS A 377 1555 1555 2.03 SSBOND 11 CYS A 355 CYS A 368 1555 1555 2.04 SSBOND 12 CYS A 402 CYS A 674 1555 1555 2.04 SSBOND 13 CYS A 450 CYS A 523 1555 1555 2.03 SSBOND 14 CYS A 474 CYS A 665 1555 1555 2.02 SSBOND 15 CYS A 484 CYS A 498 1555 1555 2.04 SSBOND 16 CYS A 495 CYS A 506 1555 1555 2.04 SSBOND 17 CYS A 563 CYS A 577 1555 1555 2.04 LINK NE2 HIS A 14 OS OS A 703 1555 1555 2.11 LINK NE2 HIS A 289 OS OS A 703 1555 1555 2.11 LINK OD1 ASP A 392 FE FE A 701 1555 1555 2.12 LINK OH TYR A 426 FE FE A 701 1555 1555 2.09 LINK OH TYR A 517 FE FE A 701 1555 1555 2.00 LINK NE2 HIS A 585 FE FE A 701 1555 1555 2.36 LINK FE FE A 701 O7 MLI A 702 1555 1555 2.14 LINK FE FE A 701 O9 MLI A 702 1555 1555 2.06 LINK OS OS A 703 O HOH A 801 1555 1555 2.11 LINK OS OS A 703 O HOH A 803 1555 1555 2.11 LINK OS OS A 703 O HOH A 809 1555 1555 2.11 LINK OS OS A 703 O HOH A 827 1555 1555 2.11 CISPEP 1 ALA A 73 PRO A 74 0 3.85 CISPEP 2 GLU A 141 PRO A 142 0 0.18 CISPEP 3 LYS A 144 PRO A 145 0 0.65 CISPEP 4 GLY A 258 LYS A 259 0 -1.26 SITE 1 AC1 5 ASP A 392 TYR A 426 TYR A 517 HIS A 585 SITE 2 AC1 5 MLI A 702 SITE 1 AC2 10 ASP A 392 TYR A 426 THR A 452 ARG A 456 SITE 2 AC2 10 THR A 457 ALA A 458 GLY A 459 TYR A 517 SITE 3 AC2 10 HIS A 585 FE A 701 SITE 1 AC3 6 HIS A 14 HIS A 289 HOH A 801 HOH A 803 SITE 2 AC3 6 HOH A 809 HOH A 827 CRYST1 137.831 156.729 107.313 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 0.007255 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009319 0.00000