HEADER TRANSPORT PROTEIN 20-AUG-17 5Y89 TITLE PERIPLASMIC HEME-BINDING PROTEIN BHUT IN COMPLEX WITH ONE HEME (HOLO- TITLE 2 1) 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 Y.NAOE,N.NAKAMURA,M.M.RAHMAN,Y.SHIRO,H.SUGIMOTO REVDAT 3 27-MAR-24 5Y89 1 REMARK REVDAT 2 22-NOV-17 5Y89 1 JRNL REVDAT 1 11-OCT-17 5Y89 0 SPRSDE 11-OCT-17 5Y89 5GJ0 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. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 50964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2706 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3671 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3902 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 109 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 1.32000 REMARK 3 B12 (A**2) : -0.20000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.174 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.046 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4197 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4072 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5775 ; 1.806 ; 2.037 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9251 ; 1.597 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 534 ; 5.508 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;30.934 ;21.484 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 593 ;15.098 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;21.184 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 652 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4864 ; 0.017 ; 0.023 REMARK 3 GENERAL PLANES OTHERS (A): 987 ; 0.021 ; 0.023 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 39 305 B 39 305 29970 0.120 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 39 A 403 REMARK 3 ORIGIN FOR THE GROUP (A): 65.2524 111.0544 3.6918 REMARK 3 T TENSOR REMARK 3 T11: 0.2121 T22: 0.2599 REMARK 3 T33: 0.2036 T12: 0.1551 REMARK 3 T13: 0.0718 T23: 0.1788 REMARK 3 L TENSOR REMARK 3 L11: 2.9894 L22: 1.2017 REMARK 3 L33: 1.2318 L12: -0.5878 REMARK 3 L13: 0.3351 L23: 0.2951 REMARK 3 S TENSOR REMARK 3 S11: 0.1255 S12: 0.3339 S13: 0.6488 REMARK 3 S21: -0.3655 S22: -0.2748 S23: -0.2444 REMARK 3 S31: -0.3307 S32: 0.0273 S33: 0.1494 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 39 B 403 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9494 113.3699 19.9835 REMARK 3 T TENSOR REMARK 3 T11: 0.1114 T22: 0.1251 REMARK 3 T33: 0.0297 T12: 0.0636 REMARK 3 T13: -0.0479 T23: -0.0333 REMARK 3 L TENSOR REMARK 3 L11: 0.5655 L22: 0.5212 REMARK 3 L33: 1.2554 L12: -0.1864 REMARK 3 L13: -0.3333 L23: 0.3966 REMARK 3 S TENSOR REMARK 3 S11: 0.0676 S12: -0.1112 S13: 0.0161 REMARK 3 S21: 0.0655 S22: 0.0981 S23: -0.0731 REMARK 3 S31: 0.1843 S32: 0.1983 S33: -0.1657 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5Y89 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_1300004751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-12; 12-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL26B1; BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00; 1.7375 REMARK 200 MONOCHROMATOR : SI(111); SI(111) REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225; RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53708 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 22.10 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 21.00 REMARK 200 R MERGE FOR SHELL (I) : 0.86000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 79.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE, PH 4.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 39.24533 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 78.49067 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 58.86800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 98.11333 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 19.62267 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.24533 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 78.49067 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 98.11333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 58.86800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 19.62267 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 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 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 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 B 532 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 GLY A 35 REMARK 465 PRO A 36 REMARK 465 LEU A 37 REMARK 465 GLY A 38 REMARK 465 GLY B 35 REMARK 465 PRO B 36 REMARK 465 LEU B 37 REMARK 465 GLY B 38 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 60 CD GLU B 60 OE2 0.088 REMARK 500 GLU B 94 CD GLU B 94 OE1 0.067 REMARK 500 SER B 98 CB SER B 98 OG 0.081 REMARK 500 GLU B 136 CD GLU B 136 OE1 0.069 REMARK 500 GLU B 231 CD GLU B 231 OE1 0.066 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 ARG A 299 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ASP B 77 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 100 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 100 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 270 CG - CD - NE ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG B 270 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 270 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG B 299 NE - CZ - NH1 ANGL. DEV. = 3.2 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 PRO A 76 -161.52 -79.44 REMARK 500 ALA A 90 48.90 -143.42 REMARK 500 ALA A 181 -124.11 -125.65 REMARK 500 ASN A 191 66.65 -159.03 REMARK 500 GLN A 196 115.22 -160.70 REMARK 500 HIS A 224 -143.43 70.28 REMARK 500 ALA B 90 47.35 -143.28 REMARK 500 ALA B 181 -122.42 -128.82 REMARK 500 ASN B 191 62.62 -158.57 REMARK 500 HIS B 224 -146.26 68.12 REMARK 500 ALA B 265 41.05 -98.14 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 87.6 REMARK 620 3 HEM A 401 NB 82.5 86.5 REMARK 620 4 HEM A 401 NC 93.5 175.1 89.0 REMARK 620 5 HEM A 401 ND 99.6 90.7 176.4 93.8 REMARK 620 N 1 2 3 4 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 87.7 REMARK 620 3 HEM A 401 NB 83.7 88.2 REMARK 620 4 HEM A 401 NC 93.0 178.1 90.1 REMARK 620 5 HEM A 401 ND 97.6 89.7 177.5 92.0 REMARK 620 N 1 2 3 4 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 88.2 REMARK 620 3 HEM B 401 NB 86.4 92.8 REMARK 620 4 HEM B 401 NC 95.6 175.7 89.5 REMARK 620 5 HEM B 401 ND 98.4 90.5 174.3 86.9 REMARK 620 N 1 2 3 4 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 89.9 REMARK 620 3 HEM B 401 NB 85.4 92.4 REMARK 620 4 HEM B 401 NC 94.8 175.3 87.1 REMARK 620 5 HEM B 401 ND 100.6 93.0 171.9 87.0 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 ACT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GIZ RELATED DB: PDB REMARK 900 HEME-FREE FORM REMARK 900 RELATED ID: 5GJ3 RELATED DB: PDB REMARK 900 HOMOLOGOUS PROTEIN IN HEME-BOUND FORM DBREF 5Y89 A 40 305 UNP B4EKB3 B4EKB3_BURCJ 40 305 DBREF 5Y89 B 40 305 UNP B4EKB3 B4EKB3_BURCJ 40 305 SEQADV 5Y89 GLY A 35 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 PRO A 36 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 LEU A 37 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 GLY A 38 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 SER A 39 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 GLY B 35 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 PRO B 36 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 LEU B 37 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 GLY B 38 UNP B4EKB3 EXPRESSION TAG SEQADV 5Y89 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 86 HET ACT A 402 4 HET SO4 A 403 5 HET HEM B 401 86 HET ACT B 402 4 HET SO4 B 403 5 HET SO4 B 404 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 5 SO4 3(O4 S 2-) FORMUL 10 HOH *176(H2 O) HELIX 1 AA1 GLY A 46 LEU A 56 1 11 HELIX 2 AA2 PRO A 76 LEU A 82 1 7 HELIX 3 AA3 SER A 92 SER A 98 1 7 HELIX 4 AA4 PRO A 112 ALA A 122 1 11 HELIX 5 AA5 ASP A 134 ASP A 150 1 17 HELIX 6 AA6 VAL A 151 ALA A 175 1 25 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 ASP A 245 GLY A 252 1 8 HELIX 10 AB1 GLY A 253 ALA A 259 1 7 HELIX 11 AB2 GLY A 262 ALA A 265 5 4 HELIX 12 AB3 THR A 266 ALA A 271 1 6 HELIX 13 AB4 ASP A 278 GLY A 284 1 7 HELIX 14 AB5 ARG A 288 ALA A 305 1 18 HELIX 15 AB6 GLY B 46 LEU B 56 1 11 HELIX 16 AB7 PRO B 76 ARG B 81 1 6 HELIX 17 AB8 SER B 92 SER B 98 1 7 HELIX 18 AB9 PRO B 112 ALA B 122 1 11 HELIX 19 AC1 ASP B 134 LEU B 149 1 16 HELIX 20 AC2 VAL B 151 ALA B 175 1 25 HELIX 21 AC3 THR B 204 ALA B 213 1 10 HELIX 22 AC4 THR B 229 ALA B 237 1 9 HELIX 23 AC5 ASP B 245 VAL B 251 1 7 HELIX 24 AC6 GLY B 253 ALA B 259 1 7 HELIX 25 AC7 THR B 266 ALA B 271 1 6 HELIX 26 AC8 ASP B 278 GLY B 284 1 7 HELIX 27 AC9 ARG B 288 ALA B 305 1 18 SHEET 1 AA1 4 TYR A 64 ALA A 69 0 SHEET 2 AA1 4 LYS A 40 ILE A 45 1 N VAL A 42 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 LEU A 190 1 N VAL A 186 O ARG A 216 SHEET 3 AA2 4 LEU A 198 ALA A 200 -1 O LEU A 198 N LEU A 190 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 LEU A 190 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 VAL A 241 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 SER B 107 1 O LEU B 105 N ILE B 45 SHEET 4 AA4 4 THR B 125 PHE B 129 1 O THR B 127 N VAL B 104 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 PRO B 227 -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 AHEM A 401 1555 1555 1.97 LINK OH TYR A 87 FE BHEM A 401 1555 1555 1.98 LINK OH TYR B 87 FE AHEM B 401 1555 1555 1.86 LINK OH TYR B 87 FE BHEM B 401 1555 1555 1.85 CISPEP 1 TYR A 75 PRO A 76 0 -3.74 CISPEP 2 GLY A 111 PRO A 112 0 7.39 CISPEP 3 TYR B 75 PRO B 76 0 -2.07 CISPEP 4 GLY B 111 PRO B 112 0 3.89 SITE 1 AC1 16 GLY A 47 THR A 72 TYR A 87 GLN A 88 SITE 2 AC1 16 ARG A 89 LEU A 190 HIS A 192 THR A 193 SITE 3 AC1 16 THR A 195 THR A 204 ALA A 205 ALA A 206 SITE 4 AC1 16 TYR A 225 ACT A 402 HOH A 502 HOH A 507 SITE 1 AC2 6 LEU A 190 HIS A 192 SER A 244 ALA A 279 SITE 2 AC2 6 HEM A 401 HOH A 514 SITE 1 AC3 5 SER A 98 THR A 229 THR A 230 HOH A 521 SITE 2 AC3 5 ARG B 161 SITE 1 AC4 16 GLY B 47 THR B 71 THR B 72 TYR B 87 SITE 2 AC4 16 GLN B 88 ARG B 89 HIS B 192 THR B 195 SITE 3 AC4 16 THR B 204 ALA B 205 ALA B 206 TYR B 225 SITE 4 AC4 16 ACT B 402 HOH B 517 HOH B 530 HOH B 612 SITE 1 AC5 7 PHE B 188 LEU B 190 HIS B 192 SER B 244 SITE 2 AC5 7 ALA B 279 HEM B 401 HOH B 539 SITE 1 AC6 4 ARG B 185 ARG B 216 GLN B 220 HOH B 509 SITE 1 AC7 3 ARG B 298 ARG B 299 ASP B 302 CRYST1 199.166 199.166 117.736 90.00 90.00 120.00 P 61 2 2 24 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 0.005021 0.002899 0.000000 0.00000 SCALE2 0.000000 0.005798 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008494 0.00000