HEADER LYASE 18-JAN-16 5HNR TITLE THE X-RAY STRUCTURE OF OCTAMERIC HUMAN NATIVE 5-AMINOLAEVULINIC ACID TITLE 2 DEHYDRATASE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DELTA-AMINOLEVULINIC ACID DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALADH,PORPHOBILINOGEN SYNTHASE; COMPND 5 EC: 4.2.1.24 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BLOOD KEYWDS TETRAPYRROLE BIOSYNTHESIS ENZYME, TIM BARREL, SUBSTRATE COMPLEX., KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.L.MILLS-DAVIES,D.THOMPSON,P.M.SHOOLINGIN-JORDAN,P.T.ERSKINE, AUTHOR 2 J.B.COOPER REVDAT 5 10-JAN-24 5HNR 1 REMARK REVDAT 4 15-NOV-23 5HNR 1 ATOM REVDAT 3 25-JAN-17 5HNR 1 JRNL REVDAT 2 11-JAN-17 5HNR 1 JRNL REVDAT 1 27-JAN-16 5HNR 0 JRNL AUTH N.MILLS-DAVIES,D.BUTLER,E.NORTON,D.THOMPSON,M.SARWAR,J.GUO, JRNL AUTH 2 R.GILL,N.AZIM,A.COKER,S.P.WOOD,P.T.ERSKINE,L.COATES, JRNL AUTH 3 J.B.COOPER,N.RASHID,M.AKHTAR,P.M.SHOOLINGIN-JORDAN JRNL TITL STRUCTURAL STUDIES OF SUBSTRATE AND PRODUCT COMPLEXES OF JRNL TITL 2 5-AMINOLAEVULINIC ACID DEHYDRATASE FROM HUMANS, ESCHERICHIA JRNL TITL 3 COLI AND THE HYPERTHERMOPHILE PYROBACULUM CALIDIFONTIS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 9 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 28045381 JRNL DOI 10.1107/S2059798316019525 REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 17779 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 872 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) : 2.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 795 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.7200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4825 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.04000 REMARK 3 B22 (A**2) : -1.04000 REMARK 3 B33 (A**2) : 2.08000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.367 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.260 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.612 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4956 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4793 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6717 ; 1.655 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11007 ; 1.224 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 618 ; 6.253 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;37.961 ;22.464 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 809 ;18.071 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;17.986 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 748 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5523 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1113 ; 0.002 ; 0.020 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): 2491 ; 4.163 ; 5.707 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2490 ; 4.159 ; 5.706 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3102 ; 6.674 ; 8.532 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3103 ; 6.674 ; 8.534 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2465 ; 4.587 ; 6.212 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2462 ; 4.588 ; 6.214 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3610 ; 7.182 ; 9.123 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5357 ;11.049 ;44.666 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5356 ;11.032 ;44.669 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 REMARK 4 REMARK 4 5HNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 - 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 180 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 54.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1AW5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN CONCENTRATION IN 10 REMARK 280 MILLIM TRIS PH 7.4, 10 MILLIM DIOTHIOTHREITOL AND 100 MICROM REMARK 280 ZINC CHLORIDE. 5 MICROLITRES OF THIS WERE MIXED WITH AN EQUAL REMARK 280 VOLUME OF 0.1 M MES PH RANGE 6.2 - 6.5, 1.0 - 1.6 M AMMONIUM REMARK 280 SULPHATE AND 0 - 10 % DIOXANE., PH 6.3, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 100.45500 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 100.45500 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 100.45500 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 100.45500 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 43980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 78500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -503.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 125.53000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 125.53000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 125.53000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 125.53000 REMARK 350 BIOMT3 4 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 GLU A 137 REMARK 465 ASN A 138 REMARK 465 GLU A 329 REMARK 465 GLU A 330 REMARK 465 ASP B 88 REMARK 465 GLU B 89 REMARK 465 ARG B 90 REMARK 465 GLY B 91 REMARK 465 SER B 92 REMARK 465 ALA B 93 REMARK 465 THR B 127 REMARK 465 SER B 128 REMARK 465 HIS B 129 REMARK 465 GLY B 130 REMARK 465 HIS B 131 REMARK 465 CYS B 132 REMARK 465 GLY B 133 REMARK 465 LEU B 134 REMARK 465 LEU B 135 REMARK 465 SER B 136 REMARK 465 GLU B 137 REMARK 465 ASN B 138 REMARK 465 GLY B 139 REMARK 465 ALA B 140 REMARK 465 PHE B 141 REMARK 465 ARG B 142 REMARK 465 LYS B 213 REMARK 465 SER B 214 REMARK 465 SER B 215 REMARK 465 PRO B 216 REMARK 465 ALA B 217 REMARK 465 PHE B 218 REMARK 465 GLY B 219 REMARK 465 ASP B 220 REMARK 465 GLU B 329 REMARK 465 GLU B 330 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 B 529 O HOH B 529 8665 0.96 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 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 309 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 309 NE - CZ - NH2 ANGL. DEV. = -3.6 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 GLN A 4 -36.85 81.88 REMARK 500 TYR A 11 42.02 -160.59 REMARK 500 THR A 23 -13.32 85.81 REMARK 500 VAL A 40 95.78 -69.25 REMARK 500 ILE A 44 50.67 -147.47 REMARK 500 GLU A 97 -132.62 51.73 REMARK 500 TYR A 224 -45.19 -139.09 REMARK 500 PRO A 253 -172.17 -69.26 REMARK 500 TRP A 326 -8.02 -53.49 REMARK 500 GLN B 4 -35.17 77.14 REMARK 500 TYR B 11 34.29 -149.90 REMARK 500 THR B 23 -23.10 82.57 REMARK 500 ILE B 44 51.31 -165.06 REMARK 500 ARG B 84 -71.91 -78.82 REMARK 500 VAL B 85 103.86 -160.91 REMARK 500 SER B 96 76.26 -163.11 REMARK 500 GLU B 97 -78.29 -121.30 REMARK 500 PRO B 125 -111.18 -78.45 REMARK 500 PRO B 253 -164.04 -70.77 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 122 SG REMARK 620 2 CYS A 124 SG 110.2 REMARK 620 3 CYS A 132 SG 108.6 100.4 REMARK 620 4 HOH A 662 O 142.9 86.2 100.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DAV A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E51 RELATED DB: PDB REMARK 900 AN EARLIER STRUCTURAL INTERPRETATION OF THE SAME DATASET. DBREF 5HNR A 1 330 UNP P13716 HEM2_HUMAN 1 330 DBREF 5HNR B 1 330 UNP P13716 HEM2_HUMAN 1 330 SEQRES 1 A 330 MET GLN PRO GLN SER VAL LEU HIS SER GLY TYR PHE HIS SEQRES 2 A 330 PRO LEU LEU ARG ALA TRP GLN THR ALA THR THR THR LEU SEQRES 3 A 330 ASN ALA SER ASN LEU ILE TYR PRO ILE PHE VAL THR ASP SEQRES 4 A 330 VAL PRO ASP ASP ILE GLN PRO ILE THR SER LEU PRO GLY SEQRES 5 A 330 VAL ALA ARG TYR GLY VAL LYS ARG LEU GLU GLU MET LEU SEQRES 6 A 330 ARG PRO LEU VAL GLU GLU GLY LEU ARG CYS VAL LEU ILE SEQRES 7 A 330 PHE GLY VAL PRO SER ARG VAL PRO LYS ASP GLU ARG GLY SEQRES 8 A 330 SER ALA ALA ASP SER GLU GLU SER PRO ALA ILE GLU ALA SEQRES 9 A 330 ILE HIS LEU LEU ARG LYS THR PHE PRO ASN LEU LEU VAL SEQRES 10 A 330 ALA CYS ASP VAL CYS LEU CYS PRO TYR THR SER HIS GLY SEQRES 11 A 330 HIS CYS GLY LEU LEU SER GLU ASN GLY ALA PHE ARG ALA SEQRES 12 A 330 GLU GLU SER ARG GLN ARG LEU ALA GLU VAL ALA LEU ALA SEQRES 13 A 330 TYR ALA LYS ALA GLY CYS GLN VAL VAL ALA PRO SER ASP SEQRES 14 A 330 MET MET ASP GLY ARG VAL GLU ALA ILE LYS GLU ALA LEU SEQRES 15 A 330 MET ALA HIS GLY LEU GLY ASN ARG VAL SER VAL MET SER SEQRES 16 A 330 TYR SER ALA LYS PHE ALA SER CYS PHE TYR GLY PRO PHE SEQRES 17 A 330 ARG ASP ALA ALA LYS SER SER PRO ALA PHE GLY ASP ARG SEQRES 18 A 330 ARG CYS TYR GLN LEU PRO PRO GLY ALA ARG GLY LEU ALA SEQRES 19 A 330 LEU ARG ALA VAL ASP ARG ASP VAL ARG GLU GLY ALA ASP SEQRES 20 A 330 MET LEU MET VAL LYS PRO GLY MET PRO TYR LEU ASP ILE SEQRES 21 A 330 VAL ARG GLU VAL LYS ASP LYS HIS PRO ASP LEU PRO LEU SEQRES 22 A 330 ALA VAL TYR HIS VAL SER GLY GLU PHE ALA MET LEU TRP SEQRES 23 A 330 HIS GLY ALA GLN ALA GLY ALA PHE ASP LEU LYS ALA ALA SEQRES 24 A 330 VAL LEU GLU ALA MET THR ALA PHE ARG ARG ALA GLY ALA SEQRES 25 A 330 ASP ILE ILE ILE THR TYR TYR THR PRO GLN LEU LEU GLN SEQRES 26 A 330 TRP LEU LYS GLU GLU SEQRES 1 B 330 MET GLN PRO GLN SER VAL LEU HIS SER GLY TYR PHE HIS SEQRES 2 B 330 PRO LEU LEU ARG ALA TRP GLN THR ALA THR THR THR LEU SEQRES 3 B 330 ASN ALA SER ASN LEU ILE TYR PRO ILE PHE VAL THR ASP SEQRES 4 B 330 VAL PRO ASP ASP ILE GLN PRO ILE THR SER LEU PRO GLY SEQRES 5 B 330 VAL ALA ARG TYR GLY VAL LYS ARG LEU GLU GLU MET LEU SEQRES 6 B 330 ARG PRO LEU VAL GLU GLU GLY LEU ARG CYS VAL LEU ILE SEQRES 7 B 330 PHE GLY VAL PRO SER ARG VAL PRO LYS ASP GLU ARG GLY SEQRES 8 B 330 SER ALA ALA ASP SER GLU GLU SER PRO ALA ILE GLU ALA SEQRES 9 B 330 ILE HIS LEU LEU ARG LYS THR PHE PRO ASN LEU LEU VAL SEQRES 10 B 330 ALA CYS ASP VAL CYS LEU CYS PRO TYR THR SER HIS GLY SEQRES 11 B 330 HIS CYS GLY LEU LEU SER GLU ASN GLY ALA PHE ARG ALA SEQRES 12 B 330 GLU GLU SER ARG GLN ARG LEU ALA GLU VAL ALA LEU ALA SEQRES 13 B 330 TYR ALA LYS ALA GLY CYS GLN VAL VAL ALA PRO SER ASP SEQRES 14 B 330 MET MET ASP GLY ARG VAL GLU ALA ILE LYS GLU ALA LEU SEQRES 15 B 330 MET ALA HIS GLY LEU GLY ASN ARG VAL SER VAL MET SER SEQRES 16 B 330 TYR SER ALA LYS PHE ALA SER CYS PHE TYR GLY PRO PHE SEQRES 17 B 330 ARG ASP ALA ALA LYS SER SER PRO ALA PHE GLY ASP ARG SEQRES 18 B 330 ARG CYS TYR GLN LEU PRO PRO GLY ALA ARG GLY LEU ALA SEQRES 19 B 330 LEU ARG ALA VAL ASP ARG ASP VAL ARG GLU GLY ALA ASP SEQRES 20 B 330 MET LEU MET VAL LYS PRO GLY MET PRO TYR LEU ASP ILE SEQRES 21 B 330 VAL ARG GLU VAL LYS ASP LYS HIS PRO ASP LEU PRO LEU SEQRES 22 B 330 ALA VAL TYR HIS VAL SER GLY GLU PHE ALA MET LEU TRP SEQRES 23 B 330 HIS GLY ALA GLN ALA GLY ALA PHE ASP LEU LYS ALA ALA SEQRES 24 B 330 VAL LEU GLU ALA MET THR ALA PHE ARG ARG ALA GLY ALA SEQRES 25 B 330 ASP ILE ILE ILE THR TYR TYR THR PRO GLN LEU LEU GLN SEQRES 26 B 330 TRP LEU LYS GLU GLU HET ZN A 501 1 HET SO4 A 502 5 HET DAV A 503 8 HET SO4 B 401 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM DAV DELTA-AMINO VALERIC ACID FORMUL 3 ZN ZN 2+ FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 DAV C5 H12 N O2 1+ FORMUL 7 HOH *120(H2 O) HELIX 1 AA1 LEU A 7 TYR A 11 5 5 HELIX 2 AA2 HIS A 13 THR A 21 1 9 HELIX 3 AA3 ASN A 27 SER A 29 5 3 HELIX 4 AA4 ARG A 60 GLU A 71 1 12 HELIX 5 AA5 SER A 99 PHE A 112 1 14 HELIX 6 AA6 ARG A 142 ALA A 160 1 19 HELIX 7 AA7 GLY A 173 HIS A 185 1 13 HELIX 8 AA8 SER A 202 PHE A 204 5 3 HELIX 9 AA9 TYR A 205 LYS A 213 1 9 HELIX 10 AB1 ALA A 230 GLY A 245 1 16 HELIX 11 AB2 GLY A 254 PRO A 256 5 3 HELIX 12 AB3 TYR A 257 HIS A 268 1 12 HELIX 13 AB4 VAL A 278 ALA A 291 1 14 HELIX 14 AB5 ASP A 295 ALA A 310 1 16 HELIX 15 AB6 TYR A 319 TRP A 326 1 8 HELIX 16 AB7 LEU B 7 TYR B 11 5 5 HELIX 17 AB8 HIS B 13 THR B 21 1 9 HELIX 18 AB9 ASN B 27 SER B 29 5 3 HELIX 19 AC1 GLY B 57 GLU B 71 1 15 HELIX 20 AC2 SER B 99 PHE B 112 1 14 HELIX 21 AC3 GLU B 145 ALA B 160 1 16 HELIX 22 AC4 GLY B 173 HIS B 185 1 13 HELIX 23 AC5 TYR B 205 ALA B 212 1 8 HELIX 24 AC6 ALA B 230 GLU B 244 1 15 HELIX 25 AC7 GLY B 254 PRO B 256 5 3 HELIX 26 AC8 TYR B 257 HIS B 268 1 12 HELIX 27 AC9 VAL B 278 ALA B 291 1 14 HELIX 28 AD1 ASP B 295 ALA B 310 1 16 HELIX 29 AD2 TYR B 319 LEU B 327 1 9 SHEET 1 AA1 7 PRO A 46 ILE A 47 0 SHEET 2 AA1 7 VAL A 53 GLY A 57 -1 O VAL A 53 N ILE A 47 SHEET 3 AA1 7 LEU A 31 THR A 38 1 N PHE A 36 O TYR A 56 SHEET 4 AA1 7 CYS A 75 VAL A 81 1 O VAL A 81 N VAL A 37 SHEET 5 AA1 7 LEU A 116 VAL A 121 1 O ALA A 118 N VAL A 76 SHEET 6 AA1 7 VAL A 164 PRO A 167 1 O ALA A 166 N VAL A 121 SHEET 7 AA1 7 SER A 192 VAL A 193 1 O SER A 192 N VAL A 165 SHEET 1 AA2 7 PRO A 46 ILE A 47 0 SHEET 2 AA2 7 VAL A 53 GLY A 57 -1 O VAL A 53 N ILE A 47 SHEET 3 AA2 7 LEU A 31 THR A 38 1 N PHE A 36 O TYR A 56 SHEET 4 AA2 7 ILE A 314 THR A 317 1 O ILE A 315 N ILE A 32 SHEET 5 AA2 7 LEU A 273 HIS A 277 1 N HIS A 277 O ILE A 316 SHEET 6 AA2 7 LEU A 249 LYS A 252 1 N LEU A 249 O ALA A 274 SHEET 7 AA2 7 ALA A 198 LYS A 199 1 N ALA A 198 O LYS A 252 SHEET 1 AA3 7 PRO B 46 ILE B 47 0 SHEET 2 AA3 7 VAL B 53 TYR B 56 -1 O VAL B 53 N ILE B 47 SHEET 3 AA3 7 LEU B 31 THR B 38 1 N THR B 38 O TYR B 56 SHEET 4 AA3 7 CYS B 75 VAL B 81 1 O VAL B 81 N VAL B 37 SHEET 5 AA3 7 LEU B 116 VAL B 121 1 O ALA B 118 N ILE B 78 SHEET 6 AA3 7 VAL B 164 PRO B 167 1 O ALA B 166 N VAL B 121 SHEET 7 AA3 7 SER B 192 VAL B 193 1 O SER B 192 N VAL B 165 SHEET 1 AA4 7 PRO B 46 ILE B 47 0 SHEET 2 AA4 7 VAL B 53 TYR B 56 -1 O VAL B 53 N ILE B 47 SHEET 3 AA4 7 LEU B 31 THR B 38 1 N THR B 38 O TYR B 56 SHEET 4 AA4 7 ILE B 314 THR B 317 1 O THR B 317 N ILE B 32 SHEET 5 AA4 7 LEU B 273 HIS B 277 1 N HIS B 277 O ILE B 316 SHEET 6 AA4 7 LEU B 249 LYS B 252 1 N LEU B 249 O ALA B 274 SHEET 7 AA4 7 ALA B 198 LYS B 199 1 N ALA B 198 O MET B 250 LINK NZ LYS A 252 CG DAV A 503 1555 1555 1.52 LINK SG CYS A 122 ZN ZN A 501 1555 1555 2.36 LINK SG CYS A 124 ZN ZN A 501 1555 1555 2.36 LINK SG CYS A 132 ZN ZN A 501 1555 1555 2.36 LINK ZN ZN A 501 O HOH A 662 1555 1555 2.03 CISPEP 1 LYS A 252 PRO A 253 0 2.33 CISPEP 2 LYS B 252 PRO B 253 0 -4.63 SITE 1 AC1 4 CYS A 122 CYS A 124 CYS A 132 HOH A 662 SITE 1 AC2 2 ARG A 17 ARG B 222 SITE 1 AC3 7 LYS A 199 TYR A 205 PHE A 208 LYS A 252 SITE 2 AC3 7 TYR A 276 SER A 279 TYR A 318 SITE 1 AC4 2 PRO B 14 ARG B 17 CRYST1 125.530 125.530 200.910 90.00 90.00 90.00 I 4 2 2 32 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 0.007966 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004977 0.00000