HEADER TRANSFERASE 18-JUN-20 7CCY
TITLE CRYSTAL STRUCTURE OF THE 2-IODOPORPHOBILINOGEN-BOUND HOLO FORM OF
TITLE 2 HUMAN HYDROXYMETHYLBILANE SYNTHASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE;
COMPND 3 CHAIN: A, C;
COMPND 4 SYNONYM: PBG-D,HYDROXYMETHYLBILANE SYNTHASE,HMBS,PRE-UROPORPHYRINOGEN
COMPND 5 SYNTHASE;
COMPND 6 EC: 2.5.1.61;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: HMBS, PBGD, UPS;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PORPHYRIN SYNTHESIS, INHIBITOR, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.SATO,M.SUGISHIMA,K.WADA,K.HIRABAYASHI,M.TSUKAGUCHI
REVDAT 2 29-NOV-23 7CCY 1 REMARK
REVDAT 1 17-MAR-21 7CCY 0
JRNL AUTH H.SATO,M.SUGISHIMA,M.TSUKAGUCHI,T.MASUKO,M.IIJIMA,M.TAKANO,
JRNL AUTH 2 Y.OMATA,K.HIRABAYASHI,K.WADA,Y.HISAEDA,K.YAMAMOTO
JRNL TITL CRYSTAL STRUCTURES OF HYDROXYMETHYLBILANE SYNTHASE COMPLEXED
JRNL TITL 2 WITH A SUBSTRATE ANALOG: A SINGLE SUBSTRATE-BINDING SITE FOR
JRNL TITL 3 FOUR CONSECUTIVE CONDENSATION STEPS.
JRNL REF BIOCHEM.J. V. 478 1023 2021
JRNL REFN ESSN 1470-8728
JRNL PMID 33600566
JRNL DOI 10.1042/BCJ20200996
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.18.2_3874
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 : GEOSTD + MONOMER LIBRARY + CDL V1.2
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.91
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 3 NUMBER OF REFLECTIONS : 25874
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.205
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.273
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1293
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 48.9100 - 4.9900 1.00 2934 155 0.1755 0.2510
REMARK 3 2 4.9900 - 3.9600 1.00 2824 149 0.1460 0.1941
REMARK 3 3 3.9600 - 3.4600 0.99 2756 144 0.1829 0.2329
REMARK 3 4 3.4600 - 3.1500 0.99 2730 143 0.2120 0.3252
REMARK 3 5 3.1500 - 2.9200 0.98 2708 143 0.2305 0.3337
REMARK 3 6 2.9200 - 2.7500 0.98 2673 140 0.2460 0.2906
REMARK 3 7 2.7500 - 2.6100 0.98 2699 142 0.2645 0.3351
REMARK 3 8 2.6100 - 2.5000 0.97 2658 139 0.2779 0.3672
REMARK 3 9 2.5000 - 2.4000 0.95 2599 138 0.2908 0.3788
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) : 0.320
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.776
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 33.75
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.64
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 : 0.010 5013
REMARK 3 ANGLE : 1.319 6812
REMARK 3 CHIRALITY : 0.067 800
REMARK 3 PLANARITY : 0.008 886
REMARK 3 DIHEDRAL : 20.908 1843
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 : 2
REMARK 3 NCS GROUP : 1
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: (chain "A" and (resid 19 through 21 or
REMARK 3 (resid 22 and (name N or name CA or name
REMARK 3 C or name O or name CB )) or resid 23
REMARK 3 through 31 or resid 33 through 127 or
REMARK 3 (resid 128 and (name N or name CA or name
REMARK 3 C or name O or name CB )) or resid 129
REMARK 3 through 134 or (resid 135 and (name N or
REMARK 3 name CA or name C or name O or name CB ))
REMARK 3 or resid 136 through 139 or (resid 140
REMARK 3 and (name N or name CA or name C or name
REMARK 3 O or name CB )) or resid 141 through 161
REMARK 3 or (resid 162 and (name N or name CA or
REMARK 3 name C or name O or name CB )) or resid
REMARK 3 163 or (resid 164 and (name N or name CA
REMARK 3 or name C or name O or name CB )) or
REMARK 3 resid 165 through 228 or (resid 229 and
REMARK 3 (name N or name CA or name C or name O or
REMARK 3 name CB )) or resid 230 through 254 or
REMARK 3 resid 256 through 272 or (resid 273 and
REMARK 3 (name N or name CA or name C or name O or
REMARK 3 name CB )) or resid 274 through 299 or
REMARK 3 resid 313 through 348 or resid 350
REMARK 3 through 354))
REMARK 3 SELECTION : (chain "C" and (resid 19 through 31 or
REMARK 3 resid 33 through 61 or (resid 62 and
REMARK 3 (name N or name CA or name C or name O or
REMARK 3 name CB )) or resid 80 through 86 or
REMARK 3 (resid 87 and (name N or name CA or name
REMARK 3 C or name O or name CB )) or resid 88
REMARK 3 through 131 or (resid 132 and (name N or
REMARK 3 name CA or name C or name O or name CB ))
REMARK 3 or resid 133 through 208 or (resid 209
REMARK 3 and (name N or name CA or name C or name
REMARK 3 O or name CB )) or resid 210 through 226
REMARK 3 or (resid 227 and (name N or name CA or
REMARK 3 name C or name O or name CB )) or resid
REMARK 3 228 through 254 or resid 256 through 257
REMARK 3 or (resid 258 and (name N or name CA or
REMARK 3 name C or name O or name CB )) or resid
REMARK 3 259 through 271 or (resid 272 through 273
REMARK 3 and (name N or name CA or name C or name
REMARK 3 O or name CB )) or resid 274 through 299
REMARK 3 or resid 313 through 348 or resid 350
REMARK 3 through 354))
REMARK 3 ATOM PAIRS NUMBER : NULL
REMARK 3 RMSD : 1.52839717372
REMARK 3 NCS GROUP : 2
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: (chain "A" and resid 401)
REMARK 3 SELECTION : (chain "C" and resid 401)
REMARK 3 ATOM PAIRS NUMBER : NULL
REMARK 3 RMSD : 0.253287830809
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7CCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-20.
REMARK 100 THE DEPOSITION ID IS D_1300017401.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-JUL-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.3
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL44XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5
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 : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25907
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 48.910
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.10200
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000
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) : 2.55
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.62300
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 3ECR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.92
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DIAMMONIUM HYDROGEN CITRATE,
REMARK 280 DITHOTHREITOL, PH 8.3, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 37.00550
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.54850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.61850
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.54850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.00550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.61850
REMARK 290 SMTRY3 4 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 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: C
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 1
REMARK 465 SER A 2
REMARK 465 GLY A 3
REMARK 465 ASN A 4
REMARK 465 GLY A 5
REMARK 465 ASN A 6
REMARK 465 ALA A 7
REMARK 465 ALA A 8
REMARK 465 ALA A 9
REMARK 465 THR A 10
REMARK 465 ALA A 11
REMARK 465 GLU A 12
REMARK 465 GLU A 13
REMARK 465 ASN A 14
REMARK 465 SER A 15
REMARK 465 PRO A 16
REMARK 465 LYS A 17
REMARK 465 MET A 18
REMARK 465 LYS A 62
REMARK 465 ILE A 63
REMARK 465 LEU A 64
REMARK 465 ASP A 65
REMARK 465 THR A 66
REMARK 465 ALA A 67
REMARK 465 LEU A 68
REMARK 465 SER A 69
REMARK 465 LYS A 70
REMARK 465 ILE A 71
REMARK 465 GLY A 72
REMARK 465 GLU A 73
REMARK 465 LYS A 74
REMARK 465 SER A 75
REMARK 465 LEU A 76
REMARK 465 PHE A 77
REMARK 465 THR A 78
REMARK 465 ARG A 355
REMARK 465 GLN A 356
REMARK 465 LEU A 357
REMARK 465 ASN A 358
REMARK 465 ASP A 359
REMARK 465 ALA A 360
REMARK 465 HIS A 361
REMARK 465 MET C 1
REMARK 465 SER C 2
REMARK 465 GLY C 3
REMARK 465 ASN C 4
REMARK 465 GLY C 5
REMARK 465 ASN C 6
REMARK 465 ALA C 7
REMARK 465 ALA C 8
REMARK 465 ALA C 9
REMARK 465 THR C 10
REMARK 465 ALA C 11
REMARK 465 GLU C 12
REMARK 465 GLU C 13
REMARK 465 ASN C 14
REMARK 465 SER C 15
REMARK 465 PRO C 16
REMARK 465 LYS C 17
REMARK 465 MET C 18
REMARK 465 LYS C 70
REMARK 465 ILE C 71
REMARK 465 GLY C 72
REMARK 465 GLU C 73
REMARK 465 LYS C 74
REMARK 465 VAL C 301
REMARK 465 PRO C 302
REMARK 465 ALA C 303
REMARK 465 GLN C 304
REMARK 465 HIS C 305
REMARK 465 GLU C 306
REMARK 465 ASP C 307
REMARK 465 GLY C 308
REMARK 465 PRO C 309
REMARK 465 GLU C 310
REMARK 465 ASP C 311
REMARK 465 ASP C 312
REMARK 465 ASN C 358
REMARK 465 ASP C 359
REMARK 465 ALA C 360
REMARK 465 HIS C 361
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 19 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 79 CG CD CE NZ
REMARK 470 GLU A 80 CG CD OE1 OE2
REMARK 470 LYS A 87 CG CD CE NZ
REMARK 470 LYS A 132 CG CD CE NZ
REMARK 470 GLU A 209 CG CD OE1 OE2
REMARK 470 LYS A 227 CG CD CE NZ
REMARK 470 GLU A 258 CG CD OE1 OE2
REMARK 470 LYS A 272 CG CD CE NZ
REMARK 470 GLN A 304 CG CD OE1 NE2
REMARK 470 GLU A 310 CG CD OE1 OE2
REMARK 470 ASP A 311 CG OD1 OD2
REMARK 470 ARG C 19 CG CD NE CZ NH1 NH2
REMARK 470 ARG C 22 CG CD NE CZ NH1 NH2
REMARK 470 LEU C 64 CG CD1 CD2
REMARK 470 ASP C 65 CG OD1 OD2
REMARK 470 THR C 66 OG1 CG2
REMARK 470 LYS C 79 CG CD CE NZ
REMARK 470 GLU C 80 CG CD OE1 OE2
REMARK 470 LYS C 128 CG CD CE NZ
REMARK 470 GLU C 135 CG CD OE1 OE2
REMARK 470 LYS C 140 CG CD CE NZ
REMARK 470 GLU C 162 CG CD OE1 OE2
REMARK 470 ARG C 164 CG CD NE CZ NH1 NH2
REMARK 470 GLN C 229 CG CD OE1 NE2
REMARK 470 ASP C 273 CG OD1 OD2
REMARK 470 GLN C 356 CG CD OE1 NE2
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 OE2 GLU A 117 O HOH A 501 2.07
REMARK 500
REMARK 500 REMARK: NULL
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 LYS C 87 CE LYS C 87 NZ 0.182
REMARK 500 LYS C 157 CE LYS C 157 NZ -0.187
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 GLU C 52 CB - CA - C ANGL. DEV. = -15.6 DEGREES
REMARK 500 GLU C 52 CA - CB - CG ANGL. DEV. = 21.5 DEGREES
REMARK 500 LYS C 87 CA - CB - CG ANGL. DEV. = 17.9 DEGREES
REMARK 500 LYS C 87 CB - CG - CD ANGL. DEV. = -18.7 DEGREES
REMARK 500 LYS C 87 CD - CE - NZ ANGL. DEV. = -27.7 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 THR A 59 -129.62 -89.53
REMARK 500 CYS A 211 100.43 -161.56
REMARK 500 SER A 262 54.01 -103.58
REMARK 500 VAL A 316 45.05 29.35
REMARK 500 THR C 66 148.17 178.18
REMARK 500 LEU C 68 39.69 -72.71
REMARK 500 THR C 145 143.58 -170.51
REMARK 500 CYS C 211 102.58 -162.18
REMARK 500 SER C 262 53.37 -104.91
REMARK 500 VAL C 316 43.44 29.92
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DPM A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue FWL C 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DPM C 402 and CYS C
REMARK 800 261
DBREF 7CCY A 1 361 UNP P08397 HEM3_HUMAN 1 361
DBREF 7CCY C 1 361 UNP P08397 HEM3_HUMAN 1 361
SEQRES 1 A 361 MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA GLU GLU
SEQRES 2 A 361 ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY THR ARG
SEQRES 3 A 361 LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER VAL VAL
SEQRES 4 A 361 ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN PHE GLU
SEQRES 5 A 361 ILE ILE ALA MET SER THR THR GLY ASP LYS ILE LEU ASP
SEQRES 6 A 361 THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU PHE THR
SEQRES 7 A 361 LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU VAL ASP
SEQRES 8 A 361 LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR VAL LEU
SEQRES 9 A 361 PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS ARG GLU
SEQRES 10 A 361 ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS PHE VAL
SEQRES 11 A 361 GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER VAL VAL
SEQRES 12 A 361 GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU GLN ARG
SEQRES 13 A 361 LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG GLY ASN
SEQRES 14 A 361 LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN GLN GLU
SEQRES 15 A 361 PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU GLN ARG
SEQRES 16 A 361 MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU HIS PRO
SEQRES 17 A 361 GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA LEU GLY
SEQRES 18 A 361 VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU ASP LEU
SEQRES 19 A 361 VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU ARG CYS
SEQRES 20 A 361 ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU GLY GLY
SEQRES 21 A 361 CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET LYS ASP
SEQRES 22 A 361 GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER LEU ASP
SEQRES 23 A 361 GLY SER ASP SER ILE GLN GLU THR MET GLN ALA THR ILE
SEQRES 24 A 361 HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU ASP ASP
SEQRES 25 A 361 PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE PRO ARG
SEQRES 26 A 361 GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SER LEU
SEQRES 27 A 361 ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN ILE LEU
SEQRES 28 A 361 ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS
SEQRES 1 C 361 MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA GLU GLU
SEQRES 2 C 361 ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY THR ARG
SEQRES 3 C 361 LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER VAL VAL
SEQRES 4 C 361 ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN PHE GLU
SEQRES 5 C 361 ILE ILE ALA MET SER THR THR GLY ASP LYS ILE LEU ASP
SEQRES 6 C 361 THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU PHE THR
SEQRES 7 C 361 LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU VAL ASP
SEQRES 8 C 361 LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR VAL LEU
SEQRES 9 C 361 PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS ARG GLU
SEQRES 10 C 361 ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS PHE VAL
SEQRES 11 C 361 GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER VAL VAL
SEQRES 12 C 361 GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU GLN ARG
SEQRES 13 C 361 LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG GLY ASN
SEQRES 14 C 361 LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN GLN GLU
SEQRES 15 C 361 PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU GLN ARG
SEQRES 16 C 361 MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU HIS PRO
SEQRES 17 C 361 GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA LEU GLY
SEQRES 18 C 361 VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU ASP LEU
SEQRES 19 C 361 VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU ARG CYS
SEQRES 20 C 361 ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU GLY GLY
SEQRES 21 C 361 CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET LYS ASP
SEQRES 22 C 361 GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER LEU ASP
SEQRES 23 C 361 GLY SER ASP SER ILE GLN GLU THR MET GLN ALA THR ILE
SEQRES 24 C 361 HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU ASP ASP
SEQRES 25 C 361 PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE PRO ARG
SEQRES 26 C 361 GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SER LEU
SEQRES 27 C 361 ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN ILE LEU
SEQRES 28 C 361 ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS
HET DPM A 401 30
HET FWL C 401 17
HET DPM C 402 30
HETNAM DPM 3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-
HETNAM 2 DPM 1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3-
HETNAM 3 DPM YL]PROPANOIC ACID
HETNAM FWL 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-2-IODO-1H-PYRROL-
HETNAM 2 FWL 3-YL]PROPANOIC ACID
HETSYN DPM DIPYRROMETHANE COFACTOR
HETSYN FWL 2-IODOPORPHOBILINOGEN
FORMUL 3 DPM 2(C20 H24 N2 O8)
FORMUL 4 FWL C10 H13 I N2 O4
FORMUL 6 HOH *64(H2 O)
HELIX 1 AA1 SER A 28 TYR A 46 1 19
HELIX 2 AA2 GLU A 80 LYS A 87 1 8
HELIX 3 AA3 LYS A 98 LEU A 100 5 3
HELIX 4 AA4 PRO A 127 VAL A 130 5 4
HELIX 5 AA5 SER A 147 PHE A 158 1 12
HELIX 6 AA6 ASN A 169 GLN A 180 1 12
HELIX 7 AA7 THR A 190 GLY A 197 1 8
HELIX 8 AA8 TRP A 198 VAL A 202 5 5
HELIX 9 AA9 ASP A 228 GLY A 236 1 9
HELIX 10 AB1 VAL A 237 HIS A 239 5 3
HELIX 11 AB2 ASP A 240 LEU A 257 1 18
HELIX 12 AB3 PRO A 324 LYS A 345 1 22
HELIX 13 AB4 GLY A 346 ALA A 354 1 9
HELIX 14 AB5 SER C 28 TYR C 46 1 19
HELIX 15 AB6 THR C 78 LYS C 87 1 10
HELIX 16 AB7 LYS C 98 LEU C 100 5 3
HELIX 17 AB8 PRO C 127 VAL C 130 5 4
HELIX 18 AB9 SER C 147 PHE C 158 1 12
HELIX 19 AC1 ASN C 169 GLN C 180 1 12
HELIX 20 AC2 THR C 190 GLY C 197 1 8
HELIX 21 AC3 TRP C 198 VAL C 202 5 5
HELIX 22 AC4 ASP C 228 GLY C 236 1 9
HELIX 23 AC5 VAL C 237 HIS C 239 5 3
HELIX 24 AC6 ASP C 240 LEU C 257 1 18
HELIX 25 AC7 PRO C 324 LYS C 345 1 22
HELIX 26 AC8 GLY C 346 LEU C 357 1 12
SHEET 1 AA1 5 GLN A 50 MET A 56 0
SHEET 2 AA1 5 VAL A 20 ARG A 26 1 N VAL A 23 O GLU A 52
SHEET 3 AA1 5 LEU A 92 SER A 96 1 O LEU A 92 N GLY A 24
SHEET 4 AA1 5 LEU A 220 ARG A 225 -1 O GLY A 221 N HIS A 95
SHEET 5 AA1 5 PHE A 108 ILE A 113 -1 N ALA A 112 O VAL A 222
SHEET 1 AA2 5 GLU A 162 ARG A 164 0
SHEET 2 AA2 5 VAL A 142 GLY A 144 1 N VAL A 143 O GLU A 162
SHEET 3 AA2 5 ALA A 185 ALA A 189 1 O ALA A 185 N GLY A 144
SHEET 4 AA2 5 ASP A 121 PHE A 125 -1 N ALA A 122 O LEU A 188
SHEET 5 AA2 5 GLN A 204 ILE A 205 -1 O GLN A 204 N VAL A 123
SHEET 1 AA3 3 VAL A 265 LYS A 272 0
SHEET 2 AA3 3 GLN A 275 TRP A 283 -1 O THR A 279 N HIS A 268
SHEET 3 AA3 3 SER A 290 THR A 298 -1 O MET A 295 N LEU A 278
SHEET 1 AA4 5 PHE C 51 MET C 56 0
SHEET 2 AA4 5 ILE C 21 ARG C 26 1 N VAL C 23 O ILE C 54
SHEET 3 AA4 5 LEU C 92 SER C 96 1 O LEU C 92 N GLY C 24
SHEET 4 AA4 5 LEU C 220 ARG C 225 -1 O GLY C 221 N HIS C 95
SHEET 5 AA4 5 PHE C 108 ILE C 113 -1 N THR C 109 O VAL C 224
SHEET 1 AA5 5 GLU C 162 ARG C 164 0
SHEET 2 AA5 5 VAL C 142 GLY C 144 1 N VAL C 143 O ARG C 164
SHEET 3 AA5 5 ALA C 185 ALA C 189 1 O ALA C 185 N GLY C 144
SHEET 4 AA5 5 ASP C 121 PHE C 125 -1 N ALA C 122 O LEU C 188
SHEET 5 AA5 5 GLN C 204 ILE C 205 -1 O GLN C 204 N VAL C 123
SHEET 1 AA6 3 VAL C 265 LYS C 272 0
SHEET 2 AA6 3 GLN C 275 TRP C 283 -1 O TYR C 277 N ALA C 270
SHEET 3 AA6 3 SER C 290 THR C 298 -1 O GLU C 293 N GLY C 280
LINK SG CYS A 261 CHA DPM A 401 1555 1555 1.77
LINK SG CYS C 261 CHA DPM C 402 1555 1555 1.77
SITE 1 AC1 16 SER A 96 LYS A 98 ASP A 99 SER A 146
SITE 2 AC1 16 SER A 147 ARG A 149 ARG A 150 ARG A 173
SITE 3 AC1 16 ALA A 189 ARG A 195 GLY A 218 CYS A 261
SITE 4 AC1 16 HOH A 503 HOH A 504 HOH A 507 HOH A 523
SITE 1 AC2 12 ARG C 26 SER C 28 GLN C 34 PHE C 77
SITE 2 AC2 12 SER C 96 ASP C 99 ARG C 167 GLY C 168
SITE 3 AC2 12 ASN C 169 LEU C 170 ARG C 173 DPM C 402
SITE 1 AC3 18 SER C 96 LYS C 98 ASP C 99 THR C 145
SITE 2 AC3 18 SER C 146 SER C 147 ARG C 149 ARG C 150
SITE 3 AC3 18 ARG C 173 LEU C 188 ALA C 189 GLY C 218
SITE 4 AC3 18 GLY C 260 SER C 262 VAL C 263 FWL C 401
SITE 5 AC3 18 HOH C 509 HOH C 519
CRYST1 74.011 81.237 109.097 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.013512 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012310 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009166 0.00000
MTRIX1 1 0.999988 -0.004013 -0.002728 -31.82894 1
MTRIX2 1 0.004048 0.999910 0.012784 0.55140 1
MTRIX3 1 0.002677 -0.012795 0.999915 18.52929 1
MTRIX1 2 0.999950 0.002629 -0.009607 -31.93691 1
MTRIX2 2 -0.001947 0.997519 0.070366 1.47106 1
MTRIX3 2 0.009768 -0.070344 0.997475 18.20039 1