HEADER TRANSPORT PROTEIN 20-AUG-17 5Y8A TITLE PERIPLASMIC HEME-BINDING PROTEIN BHUT IN COMPLEX WITH TWO HEMES (HOLO- TITLE 2 2 FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE HEMIN TRANSPORT SYSTEM, SUBSTRATE-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HEME BINDING PROTEIN, UNP RESIDUES 40-305; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CENOCEPACIA (STRAIN ATCC BAA-245 / SOURCE 3 DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610); SOURCE 4 ORGANISM_TAXID: 216591; SOURCE 5 STRAIN: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / SOURCE 6 CF5610; SOURCE 7 GENE: HMUT, BCAM2628; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS METAL TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.NAKAMURA,Y.NAOE,M.M.RAHMAN,Y.SHIRO,H.SUGIMOTO REVDAT 3 22-NOV-23 5Y8A 1 LINK REVDAT 2 22-NOV-17 5Y8A 1 JRNL REVDAT 1 11-OCT-17 5Y8A 0 SPRSDE 11-OCT-17 5Y8A 5GJ1 JRNL AUTH Y.NAOE,N.NAKAMURA,M.M.RAHMAN,T.TOSHA,S.NAGATOISHI,K.TSUMOTO, JRNL AUTH 2 Y.SHIRO,H.SUGIMOTO JRNL TITL STRUCTURAL BASIS FOR BINDING AND TRANSFER OF HEME IN JRNL TITL 2 BACTERIAL HEME-ACQUISITION SYSTEMS JRNL REF PROTEINS V. 85 2217 2017 JRNL REFN ESSN 1097-0134 JRNL PMID 28913898 JRNL DOI 10.1002/PROT.25386 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 31239 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1580 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 23.7259 - 4.4421 1.00 2810 167 0.1917 0.2399 REMARK 3 2 4.4421 - 3.5296 1.00 2715 155 0.1704 0.2235 REMARK 3 3 3.5296 - 3.0845 1.00 2722 141 0.2086 0.2728 REMARK 3 4 3.0845 - 2.8030 1.00 2752 129 0.2171 0.2671 REMARK 3 5 2.8030 - 2.6023 1.00 2721 139 0.2133 0.2762 REMARK 3 6 2.6023 - 2.4491 1.00 2697 144 0.2054 0.2509 REMARK 3 7 2.4491 - 2.3265 1.00 2668 158 0.2065 0.3107 REMARK 3 8 2.3265 - 2.2253 0.99 2697 134 0.2094 0.2450 REMARK 3 9 2.2253 - 2.1397 0.99 2660 149 0.2131 0.3153 REMARK 3 10 2.1397 - 2.0659 0.98 2663 134 0.2199 0.2912 REMARK 3 11 2.0659 - 2.0014 0.96 2554 130 0.2274 0.3093 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.99 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 : 0.009 4447 REMARK 3 ANGLE : 1.245 6140 REMARK 3 CHIRALITY : 0.054 683 REMARK 3 PLANARITY : 0.006 804 REMARK 3 DIHEDRAL : 13.720 2618 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 38 THROUGH 133) REMARK 3 ORIGIN FOR THE GROUP (A): -1.3458 28.9186 44.6259 REMARK 3 T TENSOR REMARK 3 T11: 0.2720 T22: 0.1305 REMARK 3 T33: 0.1384 T12: 0.0796 REMARK 3 T13: -0.0093 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 1.9061 L22: 2.6734 REMARK 3 L33: 0.4251 L12: -1.6462 REMARK 3 L13: -0.5486 L23: 0.2610 REMARK 3 S TENSOR REMARK 3 S11: -0.2431 S12: -0.2169 S13: -0.0453 REMARK 3 S21: 0.6765 S22: 0.3387 S23: 0.0961 REMARK 3 S31: -0.0550 S32: -0.0065 S33: 0.2411 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 134 THROUGH 180) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6469 47.6529 38.0444 REMARK 3 T TENSOR REMARK 3 T11: 0.1145 T22: -0.2910 REMARK 3 T33: 0.2767 T12: -0.0347 REMARK 3 T13: -0.0246 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.3415 L22: 1.9210 REMARK 3 L33: 0.6035 L12: -0.2320 REMARK 3 L13: -0.2878 L23: 0.3320 REMARK 3 S TENSOR REMARK 3 S11: -0.3987 S12: -0.8317 S13: 1.0375 REMARK 3 S21: 0.6644 S22: 0.1762 S23: -0.0958 REMARK 3 S31: -0.5380 S32: 0.3130 S33: 0.7017 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 181 THROUGH 305) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1259 36.1588 16.3753 REMARK 3 T TENSOR REMARK 3 T11: 0.1621 T22: 0.2513 REMARK 3 T33: 0.0854 T12: -0.0537 REMARK 3 T13: -0.0163 T23: -0.0602 REMARK 3 L TENSOR REMARK 3 L11: 2.9699 L22: 1.8130 REMARK 3 L33: 2.3572 L12: 0.4696 REMARK 3 L13: -2.2881 L23: -0.6109 REMARK 3 S TENSOR REMARK 3 S11: -0.3711 S12: 0.6145 S13: -0.3010 REMARK 3 S21: -0.2925 S22: 0.1561 S23: 0.1071 REMARK 3 S31: 0.4616 S32: -0.3211 S33: -0.1512 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 38 THROUGH 133) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9711 16.5001 41.0012 REMARK 3 T TENSOR REMARK 3 T11: 0.1470 T22: 0.1089 REMARK 3 T33: 0.1553 T12: 0.0233 REMARK 3 T13: -0.0087 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 2.3774 L22: 2.1914 REMARK 3 L33: 1.2477 L12: -0.2833 REMARK 3 L13: -0.8441 L23: 0.8130 REMARK 3 S TENSOR REMARK 3 S11: -0.0523 S12: -0.1306 S13: 0.1353 REMARK 3 S21: 0.1124 S22: 0.0635 S23: 0.0359 REMARK 3 S31: -0.1092 S32: 0.0308 S33: 0.0031 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 134 THROUGH 180) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9031 -2.6880 31.5006 REMARK 3 T TENSOR REMARK 3 T11: 0.0538 T22: -0.0049 REMARK 3 T33: 0.2784 T12: 0.0758 REMARK 3 T13: 0.0222 T23: -0.0505 REMARK 3 L TENSOR REMARK 3 L11: 1.0492 L22: 0.9742 REMARK 3 L33: 0.7319 L12: -0.5659 REMARK 3 L13: -0.4661 L23: -0.3388 REMARK 3 S TENSOR REMARK 3 S11: 0.1082 S12: -0.3167 S13: -0.6921 REMARK 3 S21: 0.3197 S22: 0.0021 S23: -0.1896 REMARK 3 S31: 0.0893 S32: 0.3601 S33: -0.2828 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 181 THROUGH 305) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6494 9.3840 13.2343 REMARK 3 T TENSOR REMARK 3 T11: 0.2652 T22: 0.3176 REMARK 3 T33: 0.0778 T12: -0.0679 REMARK 3 T13: -0.0163 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 3.0300 L22: 1.5760 REMARK 3 L33: 1.7180 L12: 0.8853 REMARK 3 L13: 1.2455 L23: 0.9998 REMARK 3 S TENSOR REMARK 3 S11: -0.3743 S12: 0.7817 S13: 0.2912 REMARK 3 S21: -0.4975 S22: 0.1420 S23: -0.0143 REMARK 3 S31: -0.6318 S32: 0.2571 S33: -0.1783 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 401 THROUGH 402) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4798 25.2976 27.7669 REMARK 3 T TENSOR REMARK 3 T11: 0.6595 T22: 0.5109 REMARK 3 T33: 0.2944 T12: 0.0271 REMARK 3 T13: 0.0166 T23: -0.0695 REMARK 3 L TENSOR REMARK 3 L11: 0.0581 L22: 0.7084 REMARK 3 L33: 0.0537 L12: 0.0917 REMARK 3 L13: 0.0011 L23: 0.1325 REMARK 3 S TENSOR REMARK 3 S11: 0.1097 S12: 0.1998 S13: 0.2025 REMARK 3 S21: -0.8467 S22: 0.0681 S23: -0.0787 REMARK 3 S31: 1.1370 S32: 0.3852 S33: -0.0138 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 401 THROUGH 402) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7459 19.8986 24.5215 REMARK 3 T TENSOR REMARK 3 T11: 0.4702 T22: 0.4558 REMARK 3 T33: 0.3682 T12: 0.0072 REMARK 3 T13: -0.0179 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 3.0331 L22: 1.3346 REMARK 3 L33: 0.5918 L12: -1.2686 REMARK 3 L13: -1.3428 L23: 0.5833 REMARK 3 S TENSOR REMARK 3 S11: -0.7529 S12: -0.0475 S13: -0.9569 REMARK 3 S21: -0.3976 S22: 0.0316 S23: 1.0128 REMARK 3 S31: -0.4380 S32: -0.8514 S33: -0.0963 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 5Y8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004753. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31283 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 REMARK 200 STARTING MODEL: 5GJ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% PEG 3350, 0.2 M CALCIUM ACETATE, REMARK 280 AND 0.1 M MES PH 6.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 35 REMARK 465 PRO A 36 REMARK 465 LEU A 37 REMARK 465 GLY B 35 REMARK 465 PRO B 36 REMARK 465 LEU B 37 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 OE1 GLN A 147 O HOH A 501 2.10 REMARK 500 OD2 ASP A 165 O HOH A 502 2.14 REMARK 500 O HOH B 623 O HOH B 631 2.18 REMARK 500 OH TYR B 64 O HOH B 501 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 624 O HOH B 642 1565 2.08 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 PRO A 76 -166.49 -79.24 REMARK 500 ALA A 181 -120.70 -126.25 REMARK 500 HIS A 192 -26.13 -154.60 REMARK 500 THR A 193 -66.05 -106.13 REMARK 500 THR A 195 45.14 -82.42 REMARK 500 THR A 195 149.72 146.26 REMARK 500 HIS A 224 -153.48 64.09 REMARK 500 GLU A 246 -83.33 -50.06 REMARK 500 ALA A 250 20.27 -74.65 REMARK 500 ALA B 181 -117.07 -130.07 REMARK 500 HIS B 192 -23.06 -159.98 REMARK 500 THR B 193 -60.48 -106.38 REMARK 500 THR B 195 158.92 154.94 REMARK 500 HIS B 224 -144.75 68.48 REMARK 500 ALA B 237 61.26 32.24 REMARK 500 ALA B 250 12.01 -67.71 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 HEM A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 87 OH REMARK 620 2 HEM A 401 NA 100.8 REMARK 620 3 HEM A 401 NB 99.5 84.6 REMARK 620 4 HEM A 401 NC 96.4 162.1 87.8 REMARK 620 5 HEM A 401 ND 97.8 88.8 162.3 93.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 271 O REMARK 620 2 HOH A 593 O 32.7 REMARK 620 3 HOH A 609 O 33.8 3.4 REMARK 620 4 ALA B 271 O 33.4 2.3 1.2 REMARK 620 5 HOH B 582 O 30.4 2.3 4.7 3.7 REMARK 620 6 HOH B 624 O 29.1 4.8 4.7 4.5 3.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR B 87 OH REMARK 620 2 HEM B 401 NA 92.3 REMARK 620 3 HEM B 401 NB 99.5 88.8 REMARK 620 4 HEM B 401 NC 102.1 165.5 90.2 REMARK 620 5 HEM B 401 ND 96.1 87.0 164.0 90.1 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 HEM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GIZ RELATED DB: PDB REMARK 900 HEME-FREE FORM OF BHUT REMARK 900 RELATED ID: 5GJ3 RELATED DB: PDB REMARK 900 TWO-HEME-BOUND FORM OF HOMOLOGOUS PROTEIN RHUT DBREF 5Y8A A 40 305 UNP B4EKB3 B4EKB3_BURCJ 40 305 DBREF 5Y8A B 40 305 UNP B4EKB3 B4EKB3_BURCJ 40 305 SEQADV 5Y8A GLY A 35 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A PRO A 36 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A LEU A 37 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A GLY A 38 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A SER A 39 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A GLY B 35 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A PRO B 36 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A LEU B 37 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A GLY B 38 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y8A SER B 39 UNP B4EKB3 EXPRESSION TAG SEQRES 1 A 271 GLY PRO LEU GLY SER LYS ARG VAL ILE VAL ILE GLY GLY SEQRES 2 A 271 ALA LEU ALA GLU THR ALA PHE ALA LEU GLY GLY ALA GLU SEQRES 3 A 271 THR PRO ARG TYR ARG LEU VAL GLY ALA ASP THR THR CYS SEQRES 4 A 271 THR TYR PRO ASP ALA ALA LYS ARG LEU PRO LYS VAL GLY SEQRES 5 A 271 TYR GLN ARG ALA LEU SER ALA GLU GLY LEU LEU SER LEU SEQRES 6 A 271 ARG PRO ASP LEU VAL LEU ALA SER ALA GLU ALA GLY PRO SEQRES 7 A 271 PRO THR ALA ILE ALA GLN VAL LYS GLY ALA GLY VAL THR SEQRES 8 A 271 VAL THR THR PHE ASP GLU ARG HIS ASP VAL GLU SER VAL SEQRES 9 A 271 ARG ALA LYS ILE THR GLY VAL ALA GLN ALA LEU ASP VAL SEQRES 10 A 271 ARG ASP ALA GLY ALA ALA LEU LEU GLN ARG PHE ASP ARG SEQRES 11 A 271 ASP TRP GLN ALA ALA ARG ASP ALA VAL ALA ALA ARG VAL SEQRES 12 A 271 PRO GLY GLY ALA GLN PRO PRO ARG VAL LEU PHE VAL LEU SEQRES 13 A 271 ASN HIS THR GLY THR GLN ALA LEU VAL ALA GLY GLN ARG SEQRES 14 A 271 THR ALA ALA ASP ALA MET ILE ARG TYR ALA GLY ALA ARG SEQRES 15 A 271 ASN ALA MET GLN GLY PHE ASP HIS TYR LYS PRO LEU THR SEQRES 16 A 271 THR GLU ALA LEU ALA ALA ALA ALA PRO ASP VAL VAL LEU SEQRES 17 A 271 ILE SER ASP GLU GLY LEU ALA ALA VAL GLY GLY HIS ALA SEQRES 18 A 271 ALA LEU LEU ALA THR PRO GLY PHE GLY ALA THR PRO ALA SEQRES 19 A 271 GLY ARG ALA ARG ARG VAL VAL SER LEU ASP ALA LEU PHE SEQRES 20 A 271 LEU LEU GLY PHE GLY PRO ARG LEU PRO LEU ALA VAL THR SEQRES 21 A 271 THR LEU HIS ARG ARG LEU SER ASP ALA LEU ALA SEQRES 1 B 271 GLY PRO LEU GLY SER LYS ARG VAL ILE VAL ILE GLY GLY SEQRES 2 B 271 ALA LEU ALA GLU THR ALA PHE ALA LEU GLY GLY ALA GLU SEQRES 3 B 271 THR PRO ARG TYR ARG LEU VAL GLY ALA ASP THR THR CYS SEQRES 4 B 271 THR TYR PRO ASP ALA ALA LYS ARG LEU PRO LYS VAL GLY SEQRES 5 B 271 TYR GLN ARG ALA LEU SER ALA GLU GLY LEU LEU SER LEU SEQRES 6 B 271 ARG PRO ASP LEU VAL LEU ALA SER ALA GLU ALA GLY PRO SEQRES 7 B 271 PRO THR ALA ILE ALA GLN VAL LYS GLY ALA GLY VAL THR SEQRES 8 B 271 VAL THR THR PHE ASP GLU ARG HIS ASP VAL GLU SER VAL SEQRES 9 B 271 ARG ALA LYS ILE THR GLY VAL ALA GLN ALA LEU ASP VAL SEQRES 10 B 271 ARG ASP ALA GLY ALA ALA LEU LEU GLN ARG PHE ASP ARG SEQRES 11 B 271 ASP TRP GLN ALA ALA ARG ASP ALA VAL ALA ALA ARG VAL SEQRES 12 B 271 PRO GLY GLY ALA GLN PRO PRO ARG VAL LEU PHE VAL LEU SEQRES 13 B 271 ASN HIS THR GLY THR GLN ALA LEU VAL ALA GLY GLN ARG SEQRES 14 B 271 THR ALA ALA ASP ALA MET ILE ARG TYR ALA GLY ALA ARG SEQRES 15 B 271 ASN ALA MET GLN GLY PHE ASP HIS TYR LYS PRO LEU THR SEQRES 16 B 271 THR GLU ALA LEU ALA ALA ALA ALA PRO ASP VAL VAL LEU SEQRES 17 B 271 ILE SER ASP GLU GLY LEU ALA ALA VAL GLY GLY HIS ALA SEQRES 18 B 271 ALA LEU LEU ALA THR PRO GLY PHE GLY ALA THR PRO ALA SEQRES 19 B 271 GLY ARG ALA ARG ARG VAL VAL SER LEU ASP ALA LEU PHE SEQRES 20 B 271 LEU LEU GLY PHE GLY PRO ARG LEU PRO LEU ALA VAL THR SEQRES 21 B 271 THR LEU HIS ARG ARG LEU SER ASP ALA LEU ALA HET HEM A 401 43 HET HEM A 402 43 HET HEM B 401 43 HET HEM B 402 43 HET CA B 403 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CA CALCIUM ION HETSYN HEM HEME FORMUL 3 HEM 4(C34 H32 FE N4 O4) FORMUL 7 CA CA 2+ FORMUL 8 HOH *267(H2 O) HELIX 1 AA1 GLY A 46 GLY A 57 1 12 HELIX 2 AA2 PRO A 76 ARG A 81 1 6 HELIX 3 AA3 SER A 92 LEU A 99 1 8 HELIX 4 AA4 PRO A 112 ALA A 122 1 11 HELIX 5 AA5 ASP A 134 LEU A 149 1 16 HELIX 6 AA6 VAL A 151 ARG A 176 1 26 HELIX 7 AA7 THR A 204 ALA A 213 1 10 HELIX 8 AA8 THR A 229 ALA A 237 1 9 HELIX 9 AA9 GLU A 246 GLY A 252 5 7 HELIX 10 AB1 GLY A 253 ALA A 259 1 7 HELIX 11 AB2 THR A 266 ARG A 272 1 7 HELIX 12 AB3 ASP A 278 GLY A 284 1 7 HELIX 13 AB4 ARG A 288 LEU A 304 1 17 HELIX 14 AB5 GLY B 46 GLY B 57 1 12 HELIX 15 AB6 PRO B 76 ARG B 81 1 6 HELIX 16 AB7 SER B 92 SER B 98 1 7 HELIX 17 AB8 PRO B 112 ALA B 122 1 11 HELIX 18 AB9 ASP B 134 ASP B 150 1 17 HELIX 19 AC1 VAL B 151 ARG B 176 1 26 HELIX 20 AC2 THR B 204 ALA B 213 1 10 HELIX 21 AC3 THR B 229 ALA B 237 1 9 HELIX 22 AC4 GLU B 246 ALA B 249 5 4 HELIX 23 AC5 GLY B 253 ALA B 259 1 7 HELIX 24 AC6 GLY B 262 ALA B 265 5 4 HELIX 25 AC7 THR B 266 ARG B 272 1 7 HELIX 26 AC8 ASP B 278 GLY B 284 1 7 HELIX 27 AC9 ARG B 288 LEU B 304 1 17 SHEET 1 AA1 4 TYR A 64 ALA A 69 0 SHEET 2 AA1 4 LYS A 40 ILE A 45 1 N LYS A 40 O ARG A 65 SHEET 3 AA1 4 LEU A 103 SER A 107 1 O LEU A 105 N ILE A 45 SHEET 4 AA1 4 THR A 125 PHE A 129 1 O THR A 127 N VAL A 104 SHEET 1 AA2 4 ARG A 216 ASN A 217 0 SHEET 2 AA2 4 ARG A 185 HIS A 192 1 N VAL A 186 O ARG A 216 SHEET 3 AA2 4 ALA A 197 ALA A 200 -1 O LEU A 198 N ASN A 191 SHEET 4 AA2 4 TYR A 225 PRO A 227 -1 O LYS A 226 N VAL A 199 SHEET 1 AA3 4 ARG A 216 ASN A 217 0 SHEET 2 AA3 4 ARG A 185 HIS A 192 1 N VAL A 186 O ARG A 216 SHEET 3 AA3 4 VAL A 240 SER A 244 1 O LEU A 242 N LEU A 187 SHEET 4 AA3 4 VAL A 274 LEU A 277 1 O VAL A 275 N ILE A 243 SHEET 1 AA4 4 TYR B 64 ALA B 69 0 SHEET 2 AA4 4 LYS B 40 ILE B 45 1 N VAL B 42 O VAL B 67 SHEET 3 AA4 4 LEU B 103 ALA B 106 1 O LEU B 105 N ILE B 45 SHEET 4 AA4 4 THR B 125 THR B 128 1 O THR B 127 N ALA B 106 SHEET 1 AA5 4 ARG B 216 ASN B 217 0 SHEET 2 AA5 4 ARG B 185 LEU B 190 1 N VAL B 186 O ARG B 216 SHEET 3 AA5 4 LEU B 198 ALA B 200 -1 O LEU B 198 N LEU B 190 SHEET 4 AA5 4 TYR B 225 LYS B 226 -1 O LYS B 226 N VAL B 199 SHEET 1 AA6 4 ARG B 216 ASN B 217 0 SHEET 2 AA6 4 ARG B 185 LEU B 190 1 N VAL B 186 O ARG B 216 SHEET 3 AA6 4 VAL B 240 SER B 244 1 O LEU B 242 N LEU B 187 SHEET 4 AA6 4 VAL B 274 LEU B 277 1 O VAL B 275 N VAL B 241 LINK OH TYR A 87 FE HEM A 401 1555 1555 2.11 LINK O ALA A 271 CA CA B 403 1555 1565 2.73 LINK O HOH A 593 CA CA B 403 1545 1555 2.37 LINK O HOH A 609 CA CA B 403 1545 1555 2.57 LINK OH TYR B 87 FE HEM B 401 1555 1555 2.06 LINK O ALA B 271 CA CA B 403 1555 1555 2.66 LINK CA CA B 403 O HOH B 582 1555 1555 2.59 LINK CA CA B 403 O HOH B 624 1555 1555 2.63 CISPEP 1 TYR A 75 PRO A 76 0 -1.07 CISPEP 2 GLY A 111 PRO A 112 0 2.83 CISPEP 3 THR A 193 GLY A 194 0 8.64 CISPEP 4 THR A 193 GLY A 194 0 8.12 CISPEP 5 GLY A 194 THR A 195 0 -5.18 CISPEP 6 GLY A 194 THR A 195 0 -19.05 CISPEP 7 TYR B 75 PRO B 76 0 -4.95 CISPEP 8 GLY B 111 PRO B 112 0 3.19 CISPEP 9 THR B 193 GLY B 194 0 9.00 CISPEP 10 THR B 193 GLY B 194 0 1.42 CISPEP 11 GLY B 194 THR B 195 0 -26.63 CISPEP 12 GLY B 194 THR B 195 0 -3.26 SITE 1 AC1 5 TYR A 87 GLN A 88 ARG A 89 HEM A 402 SITE 2 AC1 5 HOH A 559 SITE 1 AC2 12 LEU A 190 HIS A 192 THR A 195 THR A 204 SITE 2 AC2 12 ALA A 205 ALA A 206 HIS A 224 TYR A 225 SITE 3 AC2 12 LEU A 283 HEM A 401 HOH A 532 HOH A 553 SITE 1 AC3 8 THR B 71 THR B 72 TYR B 87 GLN B 88 SITE 2 AC3 8 ARG B 89 HEM B 402 HOH B 539 HOH B 555 SITE 1 AC4 9 LEU B 190 HIS B 192 THR B 195 THR B 204 SITE 2 AC4 9 ALA B 205 ALA B 206 TYR B 225 GLU B 246 SITE 3 AC4 9 HEM B 401 SITE 1 AC5 6 ALA A 271 HOH A 593 HOH A 609 ALA B 271 SITE 2 AC5 6 HOH B 582 HOH B 624 CRYST1 46.088 45.553 113.002 90.00 100.35 90.00 P 1 2 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 0.021698 0.000000 0.003963 0.00000 SCALE2 0.000000 0.021952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008996 0.00000