HEADER TRANSFERASE 18-JUN-20 7CD0
TITLE CRYSTAL STRUCTURE OF THE 2-IODOPORPHOBILINOGEN-BOUND ES2 INTERMEDIATE
TITLE 2 FORM OF HUMAN HYDROXYMETHYLBILANE SYNTHASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE;
COMPND 3 CHAIN: A, B;
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, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.SATO,M.SUGISHIMA,K.WADA,K.HIRABAYASHI,M.TSUKAGUCHI
REVDAT 3 23-OCT-24 7CD0 1 REMARK
REVDAT 2 29-NOV-23 7CD0 1 REMARK
REVDAT 1 17-MAR-21 7CD0 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. 2.31 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) : 2.31
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.25
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 32256
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.230
REMARK 3 R VALUE (WORKING SET) : 0.227
REMARK 3 FREE R VALUE : 0.277
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1612
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 45.2500 - 5.2900 1.00 2732 144 0.1923 0.2102
REMARK 3 2 5.2800 - 4.1900 1.00 2628 138 0.1710 0.2102
REMARK 3 3 4.1900 - 3.6700 1.00 2571 135 0.1937 0.2490
REMARK 3 4 3.6600 - 3.3300 1.00 2563 135 0.2161 0.3065
REMARK 3 5 3.3300 - 3.0900 1.00 2549 135 0.2447 0.3037
REMARK 3 6 3.0900 - 2.9100 1.00 2554 134 0.2522 0.2653
REMARK 3 7 2.9100 - 2.7600 1.00 2550 134 0.2769 0.3199
REMARK 3 8 2.7600 - 2.6400 1.00 2527 133 0.2923 0.3778
REMARK 3 9 2.6400 - 2.5400 1.00 2542 134 0.3201 0.3446
REMARK 3 10 2.5400 - 2.4500 1.00 2517 132 0.3436 0.4345
REMARK 3 11 2.4500 - 2.3800 1.00 2544 134 0.3456 0.4590
REMARK 3 12 2.3800 - 2.3100 0.95 2367 124 0.3702 0.4481
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) : 0.317
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.402
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 45.61
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.52
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 : 0.006 5121
REMARK 3 ANGLE : 1.011 6955
REMARK 3 CHIRALITY : 0.059 796
REMARK 3 PLANARITY : 0.009 909
REMARK 3 DIHEDRAL : 21.957 1900
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 9
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 19 THROUGH 86 )
REMARK 3 ORIGIN FOR THE GROUP (A): 2.5079 28.5323 1.3063
REMARK 3 T TENSOR
REMARK 3 T11: 0.3144 T22: 0.3659
REMARK 3 T33: 0.3422 T12: 0.0437
REMARK 3 T13: 0.0112 T23: 0.0431
REMARK 3 L TENSOR
REMARK 3 L11: 1.5026 L22: 4.5630
REMARK 3 L33: 6.5456 L12: 0.1325
REMARK 3 L13: -2.4357 L23: -1.5467
REMARK 3 S TENSOR
REMARK 3 S11: -0.1592 S12: -0.2506 S13: -0.3523
REMARK 3 S21: 0.1145 S22: 0.0428 S23: 0.1067
REMARK 3 S31: 0.8137 S32: -0.1772 S33: 0.0959
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 87 THROUGH 206 )
REMARK 3 ORIGIN FOR THE GROUP (A): -14.4449 33.3460 -13.6874
REMARK 3 T TENSOR
REMARK 3 T11: 0.2660 T22: 0.2367
REMARK 3 T33: 0.2919 T12: -0.0048
REMARK 3 T13: 0.0534 T23: 0.0080
REMARK 3 L TENSOR
REMARK 3 L11: 5.0460 L22: 0.4362
REMARK 3 L33: 6.1426 L12: 0.1594
REMARK 3 L13: 1.7724 L23: 0.7287
REMARK 3 S TENSOR
REMARK 3 S11: 0.0109 S12: 0.4831 S13: -0.1270
REMARK 3 S21: -0.0644 S22: -0.0328 S23: 0.0499
REMARK 3 S31: 0.0299 S32: -0.2152 S33: 0.0025
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 257 )
REMARK 3 ORIGIN FOR THE GROUP (A): -10.6278 39.5959 4.2618
REMARK 3 T TENSOR
REMARK 3 T11: 0.2549 T22: 0.2385
REMARK 3 T33: 0.2481 T12: -0.0607
REMARK 3 T13: 0.0104 T23: -0.0684
REMARK 3 L TENSOR
REMARK 3 L11: 6.4950 L22: 1.6871
REMARK 3 L33: 2.9071 L12: -0.7629
REMARK 3 L13: 0.8978 L23: 0.5721
REMARK 3 S TENSOR
REMARK 3 S11: 0.0402 S12: -0.1769 S13: 0.6736
REMARK 3 S21: 0.0990 S22: -0.0608 S23: -0.0411
REMARK 3 S31: -0.1410 S32: 0.1156 S33: 0.0595
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 258 THROUGH 298 )
REMARK 3 ORIGIN FOR THE GROUP (A): -24.8973 43.3866 -0.8583
REMARK 3 T TENSOR
REMARK 3 T11: 0.2113 T22: 0.4018
REMARK 3 T33: 0.2401 T12: 0.0317
REMARK 3 T13: 0.0445 T23: 0.0023
REMARK 3 L TENSOR
REMARK 3 L11: 6.4239 L22: 8.0038
REMARK 3 L33: 6.6331 L12: 2.0800
REMARK 3 L13: 1.7533 L23: 3.8021
REMARK 3 S TENSOR
REMARK 3 S11: -0.2944 S12: 0.1949 S13: 0.3400
REMARK 3 S21: 0.0113 S22: 0.0466 S23: 0.3067
REMARK 3 S31: -0.2372 S32: -0.3183 S33: 0.1835
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 299 THROUGH 358 )
REMARK 3 ORIGIN FOR THE GROUP (A): -18.4490 41.2042 9.9359
REMARK 3 T TENSOR
REMARK 3 T11: 0.2900 T22: 0.3684
REMARK 3 T33: 0.1734 T12: 0.0790
REMARK 3 T13: 0.0748 T23: 0.0130
REMARK 3 L TENSOR
REMARK 3 L11: 9.5571 L22: 3.7441
REMARK 3 L33: 5.4717 L12: 1.9768
REMARK 3 L13: 1.9439 L23: 1.0874
REMARK 3 S TENSOR
REMARK 3 S11: -0.1316 S12: -0.7310 S13: 0.1816
REMARK 3 S21: 0.0477 S22: 0.0660 S23: -0.2388
REMARK 3 S31: 0.1360 S32: 0.0444 S33: 0.0177
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 19 THROUGH 99 )
REMARK 3 ORIGIN FOR THE GROUP (A): -2.0880 22.3325 -35.9860
REMARK 3 T TENSOR
REMARK 3 T11: 0.3700 T22: 0.4150
REMARK 3 T33: 0.4225 T12: -0.0808
REMARK 3 T13: 0.0814 T23: 0.0245
REMARK 3 L TENSOR
REMARK 3 L11: 4.7081 L22: 4.1861
REMARK 3 L33: 3.0367 L12: 0.7144
REMARK 3 L13: -1.0099 L23: 1.8795
REMARK 3 S TENSOR
REMARK 3 S11: -0.2569 S12: 0.2386 S13: -0.8429
REMARK 3 S21: -0.0051 S22: -0.1154 S23: 0.0637
REMARK 3 S31: 0.4917 S32: -0.1399 S33: 0.3004
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 100 THROUGH 228 )
REMARK 3 ORIGIN FOR THE GROUP (A): 15.3519 29.1862 -21.1938
REMARK 3 T TENSOR
REMARK 3 T11: 0.2798 T22: 0.4536
REMARK 3 T33: 0.3751 T12: 0.0586
REMARK 3 T13: 0.0288 T23: 0.0930
REMARK 3 L TENSOR
REMARK 3 L11: 3.2485 L22: 1.2923
REMARK 3 L33: 5.9832 L12: 0.1166
REMARK 3 L13: 0.8253 L23: -0.0930
REMARK 3 S TENSOR
REMARK 3 S11: -0.0996 S12: -0.4122 S13: -0.1939
REMARK 3 S21: 0.2391 S22: 0.0058 S23: -0.2308
REMARK 3 S31: 0.1683 S32: 0.4321 S33: 0.0871
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 229 THROUGH 283 )
REMARK 3 ORIGIN FOR THE GROUP (A): 14.9549 35.2986 -39.1383
REMARK 3 T TENSOR
REMARK 3 T11: 0.2692 T22: 0.4306
REMARK 3 T33: 0.2712 T12: 0.0386
REMARK 3 T13: 0.0339 T23: 0.1496
REMARK 3 L TENSOR
REMARK 3 L11: 7.0790 L22: 1.9920
REMARK 3 L33: 4.1565 L12: 2.6722
REMARK 3 L13: 1.0137 L23: 0.1830
REMARK 3 S TENSOR
REMARK 3 S11: -0.0294 S12: 0.1260 S13: 0.2107
REMARK 3 S21: -0.0374 S22: -0.0328 S23: 0.0474
REMARK 3 S31: -0.2303 S32: 0.2279 S33: 0.0664
REMARK 3 TLS GROUP : 9
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 284 THROUGH 357 )
REMARK 3 ORIGIN FOR THE GROUP (A): 20.5066 35.2175 -42.4922
REMARK 3 T TENSOR
REMARK 3 T11: 0.2427 T22: 0.4331
REMARK 3 T33: 0.2833 T12: 0.0011
REMARK 3 T13: 0.0998 T23: 0.0117
REMARK 3 L TENSOR
REMARK 3 L11: 5.3766 L22: 3.8979
REMARK 3 L33: 4.5108 L12: 0.3670
REMARK 3 L13: 0.2589 L23: -1.1914
REMARK 3 S TENSOR
REMARK 3 S11: -0.1864 S12: 0.3491 S13: 0.0351
REMARK 3 S21: -0.0770 S22: 0.0947 S23: 0.0432
REMARK 3 S31: -0.1191 S32: 0.1659 S33: 0.0664
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : 1
REMARK 3 NCS GROUP : 1
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: (chain "A" and (resid 19 through 57 or
REMARK 3 resid 77 through 78 or (resid 79 through
REMARK 3 80 and (name N or name CA or name C or
REMARK 3 name O or name CB )) or resid 81 through
REMARK 3 88 or (resid 89 and (name N or name CA or
REMARK 3 name C or name O or name CB )) or resid
REMARK 3 90 through 134 or (resid 135 and (name N
REMARK 3 or name CA or name C or name O or name CB
REMARK 3 )) or resid 136 through 166 or (resid 167
REMARK 3 and (name N or name CA or name C or name
REMARK 3 O or name CB )) or resid 168 through 208
REMARK 3 or (resid 209 and (name N or name CA or
REMARK 3 name C or name O or name CB )) or resid
REMARK 3 210 through 357))
REMARK 3 SELECTION : (chain "B" and ((resid 19 and (name N or
REMARK 3 name CA or name C or name O or name CB ))
REMARK 3 or resid 20 through 49 or (resid 50 and
REMARK 3 (name N or name CA or name C or name O or
REMARK 3 name CB )) or resid 51 through 81 or
REMARK 3 (resid 82 and (name N or name CA or name
REMARK 3 C or name O or name CB )) or resid 83
REMARK 3 through 303 or (resid 304 and (name N or
REMARK 3 name CA or name C or name O or name CB ))
REMARK 3 or resid 305 through 357))
REMARK 3 ATOM PAIRS NUMBER : NULL
REMARK 3 RMSD : 0.958918539558
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7CD0 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_1300017405.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-APR-18
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 : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32296
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310
REMARK 200 RESOLUTION RANGE LOW (A) : 45.250
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.08400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.4800
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2
REMARK 200 DATA REDUNDANCY IN SHELL : 3.20
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.38800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.460
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 (%): 46.26
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DIAMMONIUM HYDROGEN CITRATE,
REMARK 280 DITHIOTHREITOL, 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 40.70800
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.42500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.68300
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.42500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.70800
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.68300
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: 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 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 THR A 58
REMARK 465 THR A 59
REMARK 465 GLY A 60
REMARK 465 ASP A 61
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 ASP A 359
REMARK 465 ALA A 360
REMARK 465 HIS A 361
REMARK 465 MET B 1
REMARK 465 SER B 2
REMARK 465 GLY B 3
REMARK 465 ASN B 4
REMARK 465 GLY B 5
REMARK 465 ASN B 6
REMARK 465 ALA B 7
REMARK 465 ALA B 8
REMARK 465 ALA B 9
REMARK 465 THR B 10
REMARK 465 ALA B 11
REMARK 465 GLU B 12
REMARK 465 GLU B 13
REMARK 465 ASN B 14
REMARK 465 SER B 15
REMARK 465 PRO B 16
REMARK 465 LYS B 17
REMARK 465 MET B 18
REMARK 465 THR B 58
REMARK 465 THR B 59
REMARK 465 GLY B 60
REMARK 465 ASP B 61
REMARK 465 LYS B 62
REMARK 465 ILE B 63
REMARK 465 LEU B 64
REMARK 465 ASP B 65
REMARK 465 THR B 66
REMARK 465 ALA B 67
REMARK 465 LEU B 68
REMARK 465 SER B 69
REMARK 465 LYS B 70
REMARK 465 ILE B 71
REMARK 465 GLY B 72
REMARK 465 GLU B 73
REMARK 465 LYS B 74
REMARK 465 SER B 75
REMARK 465 LEU B 76
REMARK 465 ASN B 358
REMARK 465 ASP B 359
REMARK 465 ALA B 360
REMARK 465 HIS B 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 GLN A 50 CG CD OE1 NE2
REMARK 470 GLU A 80 CG CD OE1 OE2
REMARK 470 GLU A 82 CG CD OE1 OE2
REMARK 470 LYS A 227 CG CD CE NZ
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 LYS B 79 CG CD CE NZ
REMARK 470 GLU B 80 CG CD OE1 OE2
REMARK 470 GLU B 89 CG CD OE1 OE2
REMARK 470 GLU B 135 CG CD OE1 OE2
REMARK 470 ARG B 167 CG CD NE CZ NH1 NH2
REMARK 470 GLU B 209 CG CD OE1 OE2
REMARK 470 LYS B 227 CG CD CE NZ
REMARK 470 LYS B 272 CG CD CE NZ
REMARK 470 GLU B 310 CG CD OE1 OE2
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 NH1 ARG B 251 O VAL B 316 2.12
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 145 136.49 -171.07
REMARK 500 SER A 262 72.52 57.89
REMARK 500 VAL A 316 43.93 37.94
REMARK 500 THR B 78 -46.82 -132.78
REMARK 500 THR B 145 139.55 -173.53
REMARK 500 SER B 262 72.47 59.22
REMARK 500 VAL B 316 44.87 38.91
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG B 26 0.22 SIDE CHAIN
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 7J8 A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue FWL B 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 7J8 B 401 and CYS B
REMARK 800 261
DBREF 7CD0 A 1 361 UNP P08397 HEM3_HUMAN 1 361
DBREF 7CD0 B 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 B 361 MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA GLU GLU
SEQRES 2 B 361 ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY THR ARG
SEQRES 3 B 361 LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER VAL VAL
SEQRES 4 B 361 ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN PHE GLU
SEQRES 5 B 361 ILE ILE ALA MET SER THR THR GLY ASP LYS ILE LEU ASP
SEQRES 6 B 361 THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU PHE THR
SEQRES 7 B 361 LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU VAL ASP
SEQRES 8 B 361 LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR VAL LEU
SEQRES 9 B 361 PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS ARG GLU
SEQRES 10 B 361 ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS PHE VAL
SEQRES 11 B 361 GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER VAL VAL
SEQRES 12 B 361 GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU GLN ARG
SEQRES 13 B 361 LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG GLY ASN
SEQRES 14 B 361 LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN GLN GLU
SEQRES 15 B 361 PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU GLN ARG
SEQRES 16 B 361 MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU HIS PRO
SEQRES 17 B 361 GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA LEU GLY
SEQRES 18 B 361 VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU ASP LEU
SEQRES 19 B 361 VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU ARG CYS
SEQRES 20 B 361 ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU GLY GLY
SEQRES 21 B 361 CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET LYS ASP
SEQRES 22 B 361 GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER LEU ASP
SEQRES 23 B 361 GLY SER ASP SER ILE GLN GLU THR MET GLN ALA THR ILE
SEQRES 24 B 361 HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU ASP ASP
SEQRES 25 B 361 PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE PRO ARG
SEQRES 26 B 361 GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SER LEU
SEQRES 27 B 361 ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN ILE LEU
SEQRES 28 B 361 ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS
HET 7J8 A 401 60
HET 7J8 B 401 60
HET FWL B 402 17
HETNAM 7J8 3-[4-(2-HYDROXY-2-OXOETHYL)-5-[[4-(2-HYDROXY-2-
HETNAM 2 7J8 OXOETHYL)-5-[[4-(2-HYDROXY-2-OXOETHYL)-5-[[4-(2-
HETNAM 3 7J8 HYDROXY-2-OXOETHYL)-3-(3-HYDROXY-3-OXOPROPYL)-5-
HETNAM 4 7J8 METHYL-1~{H}-PYRROL-2-YL]METHYL]-3-(3-HYDROXY-3-
HETNAM 5 7J8 OXOPROPYL)-1~{H}-PYRROL-2-YL]METHYL]-3-(3-HYDROXY-3-
HETNAM 6 7J8 OXOPROPYL)-1~{H}-PYRROL-2-YL]METHYL]-1~{H}-PYRROL-3-
HETNAM 7 7J8 YL]PROPANOIC ACID
HETNAM FWL 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-2-IODO-1H-PYRROL-
HETNAM 2 FWL 3-YL]PROPANOIC ACID
HETSYN FWL 2-IODOPORPHOBILINOGEN
FORMUL 3 7J8 2(C40 H46 N4 O16)
FORMUL 5 FWL C10 H13 I N2 O4
FORMUL 6 HOH *76(H2 O)
HELIX 1 AA1 SER A 28 TYR A 46 1 19
HELIX 2 AA2 PHE A 77 LYS A 87 1 11
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 MET A 196 1 7
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 GLU A 258 1 19
HELIX 12 AB3 PRO A 324 LYS A 345 1 22
HELIX 13 AB4 GLY A 346 LEU A 357 1 12
HELIX 14 AB5 SER B 28 TYR B 46 1 19
HELIX 15 AB6 THR B 78 LYS B 87 1 10
HELIX 16 AB7 LYS B 98 LEU B 100 5 3
HELIX 17 AB8 PRO B 127 VAL B 130 5 4
HELIX 18 AB9 SER B 147 PHE B 158 1 12
HELIX 19 AC1 ASN B 169 GLN B 180 1 12
HELIX 20 AC2 THR B 190 MET B 196 1 7
HELIX 21 AC3 TRP B 198 VAL B 202 5 5
HELIX 22 AC4 ASP B 228 GLY B 236 1 9
HELIX 23 AC5 VAL B 237 HIS B 239 5 3
HELIX 24 AC6 ASP B 240 GLU B 258 1 19
HELIX 25 AC7 PRO B 324 LYS B 345 1 22
HELIX 26 AC8 GLY B 346 GLN B 356 1 11
SHEET 1 AA1 5 PHE A 51 MET A 56 0
SHEET 2 AA1 5 ILE A 21 ARG A 26 1 N VAL A 23 O ILE A 54
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 GLU A 223 N VAL A 93
SHEET 5 AA1 5 PHE A 108 ILE A 113 -1 N THR A 109 O VAL A 224
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 ILE A 187 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 ALA A 297 N LEU A 276
SHEET 1 AA4 5 PHE B 51 MET B 56 0
SHEET 2 AA4 5 ILE B 21 ARG B 26 1 N VAL B 23 O ILE B 54
SHEET 3 AA4 5 LEU B 92 SER B 96 1 O LEU B 92 N GLY B 24
SHEET 4 AA4 5 LEU B 220 ARG B 225 -1 O GLY B 221 N HIS B 95
SHEET 5 AA4 5 PHE B 108 ILE B 113 -1 N THR B 109 O VAL B 224
SHEET 1 AA5 5 GLU B 162 ARG B 164 0
SHEET 2 AA5 5 VAL B 142 GLY B 144 1 N VAL B 143 O ARG B 164
SHEET 3 AA5 5 ALA B 185 ALA B 189 1 O ALA B 185 N GLY B 144
SHEET 4 AA5 5 ASP B 121 PHE B 125 -1 N ALA B 122 O LEU B 188
SHEET 5 AA5 5 GLN B 204 ILE B 205 -1 O GLN B 204 N VAL B 123
SHEET 1 AA6 3 VAL B 265 LYS B 272 0
SHEET 2 AA6 3 GLN B 275 TRP B 283 -1 O THR B 279 N HIS B 268
SHEET 3 AA6 3 SER B 290 THR B 298 -1 O ALA B 297 N LEU B 276
LINK SG CYS A 261 C 7J8 A 401 1555 1555 1.77
LINK SG CYS B 261 C 7J8 B 401 1555 1555 1.77
SITE 1 AC1 25 SER A 96 LYS A 98 ASP A 99 LEU A 100
SITE 2 AC1 25 PRO A 101 THR A 102 SER A 146 SER A 147
SITE 3 AC1 25 ARG A 149 ARG A 150 ARG A 173 LEU A 188
SITE 4 AC1 25 ALA A 189 ARG A 195 VAL A 215 GLY A 218
SITE 5 AC1 25 LEU A 254 GLY A 260 CYS A 261 SER A 262
SITE 6 AC1 25 HOH A 501 HOH A 513 HOH A 529 HOH A 533
SITE 7 AC1 25 HOH A 539
SITE 1 AC2 8 SER B 28 LEU B 30 GLN B 34 ASP B 99
SITE 2 AC2 8 GLY B 168 ASN B 169 LEU B 170 ARG B 173
SITE 1 AC3 23 GLN B 34 SER B 96 LYS B 98 ASP B 99
SITE 2 AC3 23 PRO B 101 THR B 102 THR B 145 SER B 146
SITE 3 AC3 23 SER B 147 ARG B 149 ARG B 150 ARG B 173
SITE 4 AC3 23 LEU B 188 ALA B 189 ARG B 195 VAL B 215
SITE 5 AC3 23 GLY B 218 LEU B 254 GLY B 260 SER B 262
SITE 6 AC3 23 VAL B 263 HOH B 503 HOH B 516
CRYST1 81.416 81.366 108.850 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 0.012283 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012290 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009187 0.00000
MTRIX1 1 -0.999902 0.008060 -0.011435 -0.26390 1
MTRIX2 1 0.008697 0.998343 -0.056875 -6.12386 1
MTRIX3 1 0.010958 -0.056969 -0.998316 -32.30187 1