PDB Short entry for 4XZD HEADER HEME BINDING PROTEIN 04-FEB-15 4XZD TITLE CRYSTAL STRUCTURE OF WILD-TYPE HASA FROM YERSINIA PSEUDOTUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTRACELLULAR HEME ACQUISITION HEMOPHORE HASA; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PSEUDOTUBERCULOSIS IP 32953; SOURCE 3 ORGANISM_TAXID: 273123; SOURCE 4 STRAIN: IP32953; SOURCE 5 GENE: HASA, YPTB0114; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS HEME ACQUISITION SYSTEM, HEMOPHORE, HEME BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KANADANI,T.HINO,S.NAGANO,T.SATO,S.OZAKI REVDAT 4 08-NOV-23 4XZD 1 LINK REVDAT 3 05-FEB-20 4XZD 1 JRNL REMARK REVDAT 2 06-JAN-16 4XZD 1 JRNL REVDAT 1 12-AUG-15 4XZD 0 JRNL AUTH M.KANADANI,T.SATO,T.HINO,S.NAGANO,S.OZAKI JRNL TITL THE CRYSTAL STRUCTURE OF HEME ACQUISITION SYSTEM A FROM JRNL TITL 2 YERSINIA PSEUDOTUBERCULOSIS (HASAYPT): ROLES OF THE AXIAL JRNL TITL 3 LIGAND TYR75 AND TWO DISTAL ARGININES IN HEME BINDING JRNL REF J.INORG.BIOCHEM. V. 151 26 2015 JRNL REFN ISSN 0162-0134 JRNL PMID 26210321 JRNL DOI 10.1016/J.JINORGBIO.2015.07.007 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 45923 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2386 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 35.6638 - 4.3687 1.00 2649 156 0.1604 0.1994 REMARK 3 2 4.3687 - 3.4685 0.99 2585 125 0.1328 0.1594 REMARK 3 3 3.4685 - 3.0303 0.99 2569 139 0.1479 0.1832 REMARK 3 4 3.0303 - 2.7534 1.00 2593 131 0.1635 0.2182 REMARK 3 5 2.7534 - 2.5561 0.99 2551 144 0.1708 0.2205 REMARK 3 6 2.5561 - 2.4054 1.00 2529 160 0.1708 0.2179 REMARK 3 7 2.4054 - 2.2850 1.00 2568 141 0.1703 0.2413 REMARK 3 8 2.2850 - 2.1855 1.00 2528 160 0.1741 0.2619 REMARK 3 9 2.1855 - 2.1014 1.00 2554 130 0.1730 0.2011 REMARK 3 10 2.1014 - 2.0289 1.00 2575 134 0.1835 0.2264 REMARK 3 11 2.0289 - 1.9654 1.00 2563 132 0.1868 0.2573 REMARK 3 12 1.9654 - 1.9093 1.00 2540 151 0.2055 0.2595 REMARK 3 13 1.9093 - 1.8590 1.00 2554 144 0.2217 0.2635 REMARK 3 14 1.8590 - 1.8137 0.99 2518 153 0.2430 0.2735 REMARK 3 15 1.8137 - 1.7724 1.00 2542 132 0.2426 0.2987 REMARK 3 16 1.7724 - 1.7347 1.00 2555 140 0.2487 0.2843 REMARK 3 17 1.7347 - 1.7000 1.00 2564 114 0.2636 0.3131 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.014 2902 REMARK 3 ANGLE : 1.648 3942 REMARK 3 CHIRALITY : 0.092 392 REMARK 3 PLANARITY : 0.009 518 REMARK 3 DIHEDRAL : 17.586 1036 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 4XZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9300 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALA 3.3.21 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45941 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 81.338 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 REMARK 200 R SYM FOR SHELL (I) : 0.55500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.0.05 REMARK 200 STARTING MODEL: 1DK0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS HCL, 1.1 M NA-CITRATE, 1.5% REMARK 280 1,6-HEXANDIOL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.62500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 MET A -11 REMARK 465 ARG A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 181 REMARK 465 GLY A 182 REMARK 465 TYR A 183 REMARK 465 MET A 184 REMARK 465 SER A 185 REMARK 465 ASP A 186 REMARK 465 ALA A 187 REMARK 465 PRO A 188 REMARK 465 MET A 189 REMARK 465 VAL A 190 REMARK 465 ASP A 191 REMARK 465 THR A 192 REMARK 465 VAL A 193 REMARK 465 GLY A 194 REMARK 465 VAL A 195 REMARK 465 MET A 196 REMARK 465 ASP A 197 REMARK 465 SER A 198 REMARK 465 ASN A 199 REMARK 465 ASP A 200 REMARK 465 MET A 201 REMARK 465 LEU A 202 REMARK 465 LEU A 203 REMARK 465 ALA A 204 REMARK 465 ALA A 205 REMARK 465 MET D -11 REMARK 465 ARG D -10 REMARK 465 GLY D -9 REMARK 465 SER D -8 REMARK 465 HIS D -7 REMARK 465 HIS D -6 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 HIS D -3 REMARK 465 HIS D -2 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 MET D 1 REMARK 465 SER D 181 REMARK 465 GLY D 182 REMARK 465 TYR D 183 REMARK 465 MET D 184 REMARK 465 SER D 185 REMARK 465 ASP D 186 REMARK 465 ALA D 187 REMARK 465 PRO D 188 REMARK 465 MET D 189 REMARK 465 VAL D 190 REMARK 465 ASP D 191 REMARK 465 THR D 192 REMARK 465 VAL D 193 REMARK 465 GLY D 194 REMARK 465 VAL D 195 REMARK 465 MET D 196 REMARK 465 ASP D 197 REMARK 465 SER D 198 REMARK 465 ASN D 199 REMARK 465 ASP D 200 REMARK 465 MET D 201 REMARK 465 LEU D 202 REMARK 465 LEU D 203 REMARK 465 ALA D 204 REMARK 465 ALA D 205 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 O HOH D 552 O HOH D 575 1.95 REMARK 500 O HOH D 552 O HOH D 577 1.97 REMARK 500 O HOH D 597 O HOH D 609 1.98 REMARK 500 O HOH D 594 O HOH D 647 2.03 REMARK 500 O HOH D 554 O HOH D 615 2.04 REMARK 500 O HOH D 456 O HOH D 469 2.05 REMARK 500 O HOH A 563 O HOH A 629 2.05 REMARK 500 O HOH D 410 O HOH D 419 2.06 REMARK 500 O HOH A 517 O HOH A 572 2.06 REMARK 500 O HOH A 571 O HOH A 600 2.07 REMARK 500 O HOH D 462 O HOH D 464 2.07 REMARK 500 O HOH A 560 O HOH A 649 2.07 REMARK 500 O HOH A 556 O HOH A 585 2.08 REMARK 500 O HOH A 468 O HOH A 492 2.08 REMARK 500 O HOH D 480 O HOH D 617 2.08 REMARK 500 O HOH A 616 O HOH A 666 2.09 REMARK 500 O HOH D 628 O HOH D 646 2.10 REMARK 500 O HOH D 553 O HOH D 598 2.10 REMARK 500 O HOH A 591 O HOH A 631 2.11 REMARK 500 O HOH A 472 O HOH A 476 2.11 REMARK 500 O HOH D 625 O HOH D 639 2.11 REMARK 500 O HOH D 647 O HOH D 651 2.12 REMARK 500 O HOH A 407 O HOH A 588 2.12 REMARK 500 O HOH D 558 O HOH D 586 2.13 REMARK 500 O HOH D 524 O HOH D 618 2.13 REMARK 500 N SER A 2 O HOH A 616 2.14 REMARK 500 O HOH A 495 O HOH A 498 2.14 REMARK 500 N SER A 2 O HOH A 666 2.14 REMARK 500 O HOH A 535 O HOH A 580 2.14 REMARK 500 O HOH D 627 O HOH D 632 2.14 REMARK 500 O HOH A 557 O HOH A 626 2.14 REMARK 500 O HOH A 637 O HOH D 567 2.15 REMARK 500 O HOH A 545 O HOH A 676 2.15 REMARK 500 O ASP D 120 O HOH D 560 2.15 REMARK 500 O HOH D 527 O HOH D 571 2.16 REMARK 500 O HOH D 560 O HOH D 649 2.16 REMARK 500 O HOH D 463 O HOH D 468 2.16 REMARK 500 O HOH A 618 O HOH A 659 2.16 REMARK 500 O HOH A 672 O HOH A 684 2.16 REMARK 500 O HOH D 477 O HOH D 620 2.17 REMARK 500 O HOH D 486 O HOH D 601 2.17 REMARK 500 OD1 ASP D 138 O HOH D 645 2.18 REMARK 500 O HOH A 584 O HOH A 610 2.19 REMARK 500 O HOH A 545 O HOH A 671 2.19 REMARK 500 O HOH A 528 O HOH A 576 2.19 REMARK 500 O HOH A 519 O HOH A 556 2.19 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 O HOH A 450 O HOH A 470 2656 2.09 REMARK 500 O HOH D 450 O HOH D 471 2555 2.10 REMARK 500 O HOH D 436 O HOH D 466 2555 2.10 REMARK 500 O HOH A 428 O HOH A 490 2656 2.14 REMARK 500 O HOH D 415 O HOH D 441 2555 2.15 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 PRO D 103 C - N - CA ANGL. DEV. = 9.5 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 PHE A 77 -140.59 48.46 REMARK 500 ASP A 95 63.77 67.81 REMARK 500 LYS A 170 -34.51 -34.07 REMARK 500 PHE D 77 -143.95 46.75 REMARK 500 ASP D 95 63.64 67.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 102 PRO A 103 -144.32 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 A 667 DISTANCE = 8.46 ANGSTROMS REMARK 525 HOH A 672 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A 677 DISTANCE = 9.96 ANGSTROMS REMARK 525 HOH A 679 DISTANCE = 7.77 ANGSTROMS REMARK 525 HOH A 685 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH D 554 DISTANCE = 8.51 ANGSTROMS REMARK 525 HOH D 566 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH D 615 DISTANCE = 8.77 ANGSTROMS REMARK 525 HOH D 650 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH D 654 DISTANCE = 8.46 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 HEM A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 75 OH REMARK 620 2 HEM A 301 NA 98.7 REMARK 620 3 HEM A 301 NB 95.1 89.8 REMARK 620 4 HEM A 301 NC 96.3 165.0 88.1 REMARK 620 5 HEM A 301 ND 100.7 89.3 164.0 88.7 REMARK 620 6 HOH A 562 O 175.3 78.0 81.5 86.9 82.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM D 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR D 75 OH REMARK 620 2 HEM D 301 NA 98.1 REMARK 620 3 HEM D 301 NB 97.9 90.9 REMARK 620 4 HEM D 301 NC 98.5 163.3 88.1 REMARK 620 5 HEM D 301 ND 99.4 86.5 162.7 89.5 REMARK 620 6 HOH D 544 O 169.2 76.3 73.1 87.5 89.6 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 HEM A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y4S RELATED DB: PDB REMARK 900 4Y4S IS Y75A MUTANT HASA DIMER FROM YERSINIA PSEUDOTUBERCULOSIS. REMARK 900 RELATED ID: 4Y1Q RELATED DB: PDB REMARK 900 4Y1Q IS Y75A MUTANT HASA MONOMER FROM YERSINIA PSEUDOTUBERCULOSIS. DBREF 4XZD A 1 205 UNP Q66G68 Q66G68_YERPS 1 205 DBREF 4XZD D 1 205 UNP Q66G68 Q66G68_YERPS 1 205 SEQADV 4XZD MET A -11 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD ARG A -10 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD GLY A -9 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD SER A -8 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS A -7 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS A -6 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS A -5 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS A -4 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS A -3 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS A -2 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD GLY A -1 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD SER A 0 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD MET D -11 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD ARG D -10 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD GLY D -9 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD SER D -8 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS D -7 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS D -6 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS D -5 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS D -4 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS D -3 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD HIS D -2 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD GLY D -1 UNP Q66G68 EXPRESSION TAG SEQADV 4XZD SER D 0 UNP Q66G68 EXPRESSION TAG SEQRES 1 A 217 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET SEQRES 2 A 217 SER THR THR ILE GLN TYR ASN SER ASN TYR ALA ASP TYR SEQRES 3 A 217 SER ILE SER SER TYR LEU ARG GLU TRP ALA ASN ASN PHE SEQRES 4 A 217 GLY ASP ILE ASP GLN ALA PRO ALA GLU THR LYS ASP ARG SEQRES 5 A 217 GLY SER PHE SER GLY SER SER THR LEU PHE SER GLY THR SEQRES 6 A 217 GLN TYR ALA ILE GLY SER SER HIS SER ASN PRO GLU GLY SEQRES 7 A 217 MET ILE ALA GLU GLY ASP LEU LYS TYR SER PHE MET PRO SEQRES 8 A 217 GLN HIS THR PHE HIS GLY GLN ILE ASP THR LEU GLN PHE SEQRES 9 A 217 GLY LYS ASP LEU ALA THR ASN ALA GLY GLY PRO SER ALA SEQRES 10 A 217 GLY LYS HIS LEU GLU LYS ILE ASP ILE THR PHE ASN GLU SEQRES 11 A 217 LEU ASP LEU SER GLY GLU PHE ASP SER GLY LYS SER MET SEQRES 12 A 217 THR GLU ASN HIS GLN GLY ASP MET HIS LYS SER VAL ARG SEQRES 13 A 217 GLY LEU MET LYS GLY ASN PRO ASP PRO MET LEU GLU VAL SEQRES 14 A 217 MET LYS ALA LYS GLY ILE ASN VAL ASP THR ALA PHE LYS SEQRES 15 A 217 ASP LEU SER ILE ALA SER GLN TYR PRO ASP SER GLY TYR SEQRES 16 A 217 MET SER ASP ALA PRO MET VAL ASP THR VAL GLY VAL MET SEQRES 17 A 217 ASP SER ASN ASP MET LEU LEU ALA ALA SEQRES 1 D 217 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET SEQRES 2 D 217 SER THR THR ILE GLN TYR ASN SER ASN TYR ALA ASP TYR SEQRES 3 D 217 SER ILE SER SER TYR LEU ARG GLU TRP ALA ASN ASN PHE SEQRES 4 D 217 GLY ASP ILE ASP GLN ALA PRO ALA GLU THR LYS ASP ARG SEQRES 5 D 217 GLY SER PHE SER GLY SER SER THR LEU PHE SER GLY THR SEQRES 6 D 217 GLN TYR ALA ILE GLY SER SER HIS SER ASN PRO GLU GLY SEQRES 7 D 217 MET ILE ALA GLU GLY ASP LEU LYS TYR SER PHE MET PRO SEQRES 8 D 217 GLN HIS THR PHE HIS GLY GLN ILE ASP THR LEU GLN PHE SEQRES 9 D 217 GLY LYS ASP LEU ALA THR ASN ALA GLY GLY PRO SER ALA SEQRES 10 D 217 GLY LYS HIS LEU GLU LYS ILE ASP ILE THR PHE ASN GLU SEQRES 11 D 217 LEU ASP LEU SER GLY GLU PHE ASP SER GLY LYS SER MET SEQRES 12 D 217 THR GLU ASN HIS GLN GLY ASP MET HIS LYS SER VAL ARG SEQRES 13 D 217 GLY LEU MET LYS GLY ASN PRO ASP PRO MET LEU GLU VAL SEQRES 14 D 217 MET LYS ALA LYS GLY ILE ASN VAL ASP THR ALA PHE LYS SEQRES 15 D 217 ASP LEU SER ILE ALA SER GLN TYR PRO ASP SER GLY TYR SEQRES 16 D 217 MET SER ASP ALA PRO MET VAL ASP THR VAL GLY VAL MET SEQRES 17 D 217 ASP SER ASN ASP MET LEU LEU ALA ALA HET HEM A 301 43 HET HEM D 301 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *551(H2 O) HELIX 1 AA1 SER A 9 ALA A 12 5 4 HELIX 2 AA2 SER A 15 GLY A 28 1 14 HELIX 3 AA3 ASP A 29 ALA A 33 5 5 HELIX 4 AA4 PRO A 34 LYS A 38 5 5 HELIX 5 AA5 SER A 130 HIS A 135 1 6 HELIX 6 AA6 GLY A 137 LYS A 148 1 12 HELIX 7 AA7 PRO A 151 GLY A 162 1 12 HELIX 8 AA8 ALA A 168 LEU A 172 5 5 HELIX 9 AA9 SER D 9 ALA D 12 5 4 HELIX 10 AB1 SER D 15 GLY D 28 1 14 HELIX 11 AB2 ASP D 29 ALA D 33 5 5 HELIX 12 AB3 PRO D 34 LYS D 38 5 5 HELIX 13 AB4 SER D 130 HIS D 135 1 6 HELIX 14 AB5 GLY D 137 LYS D 148 1 12 HELIX 15 AB6 PRO D 151 LYS D 161 1 11 HELIX 16 AB7 ALA D 168 LEU D 172 5 5 SHEET 1 AA1 7 SER A 42 PHE A 43 0 SHEET 2 AA1 7 SER A 51 GLY A 58 -1 O ALA A 56 N SER A 42 SHEET 3 AA1 7 GLU A 65 TYR A 75 -1 O ALA A 69 N TYR A 55 SHEET 4 AA1 7 PHE A 83 THR A 98 -1 O HIS A 84 N LYS A 74 SHEET 5 AA1 7 LYS A 107 GLY A 123 -1 O PHE A 116 N LEU A 90 SHEET 6 AA1 7 THR A 4 TYR A 7 -1 N THR A 4 O ASN A 117 SHEET 7 AA1 7 ALA A 175 GLN A 177 1 O SER A 176 N ILE A 5 SHEET 1 AA2 5 SER D 42 PHE D 43 0 SHEET 2 AA2 5 SER D 51 GLY D 58 -1 O ALA D 56 N SER D 42 SHEET 3 AA2 5 GLU D 65 TYR D 75 -1 O ALA D 69 N TYR D 55 SHEET 4 AA2 5 PHE D 83 THR D 98 -1 O HIS D 84 N LYS D 74 SHEET 5 AA2 5 LEU D 121 GLY D 123 -1 O LEU D 121 N ILE D 87 SHEET 1 AA3 7 SER D 42 PHE D 43 0 SHEET 2 AA3 7 SER D 51 GLY D 58 -1 O ALA D 56 N SER D 42 SHEET 3 AA3 7 GLU D 65 TYR D 75 -1 O ALA D 69 N TYR D 55 SHEET 4 AA3 7 PHE D 83 THR D 98 -1 O HIS D 84 N LYS D 74 SHEET 5 AA3 7 LYS D 107 ASN D 117 -1 O PHE D 116 N LEU D 90 SHEET 6 AA3 7 THR D 4 TYR D 7 -1 N THR D 4 O ASN D 117 SHEET 7 AA3 7 ALA D 175 GLN D 177 1 O SER D 176 N ILE D 5 LINK OH TYR A 75 FE HEM A 301 1555 1555 2.16 LINK FE HEM A 301 O HOH A 562 1555 1555 2.69 LINK OH TYR D 75 FE HEM D 301 1555 1555 2.11 LINK FE HEM D 301 O HOH D 544 1555 1555 2.67 CISPEP 1 MET A 78 PRO A 79 0 3.31 CISPEP 2 MET D 78 PRO D 79 0 -2.37 SITE 1 AC1 14 ARG A 40 GLY A 41 TYR A 55 TYR A 75 SITE 2 AC1 14 HIS A 81 PHE A 83 MET A 131 HIS A 140 SITE 3 AC1 14 ARG A 144 MET A 147 HOH A 529 HOH A 562 SITE 4 AC1 14 HOH A 609 LEU D 49 SITE 1 AC2 13 LEU A 49 ARG D 40 GLY D 41 TYR D 55 SITE 2 AC2 13 TYR D 75 HIS D 81 PHE D 83 ARG D 144 SITE 3 AC2 13 MET D 147 HOH D 494 HOH D 502 HOH D 544 SITE 4 AC2 13 HOH D 573 CRYST1 48.740 53.250 82.580 90.00 99.95 90.00 P 1 21 1 4 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 0.020517 0.000000 0.003599 0.00000 SCALE2 0.000000 0.018779 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012294 0.00000