HEADER TRANSFERASE 18-JUN-20 7CCX
TITLE CRYSTAL STRUCTURE OF THE HOLO FORM OF HUMAN HYDROXYMETHYLBILANE
TITLE 2 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, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.SATO,M.SUGISHIMA,K.WADA,K.HIRABAYASHI,M.TSUKAGUCHI
REVDAT 2 29-NOV-23 7CCX 1 REMARK
REVDAT 1 17-MAR-21 7CCX 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. 1.84 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.14_3260
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 : CDL V1.2
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.15
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 3 NUMBER OF REFLECTIONS : 53344
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.196
REMARK 3 R VALUE (WORKING SET) : 0.194
REMARK 3 FREE R VALUE : 0.247
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.740
REMARK 3 FREE R VALUE TEST SET COUNT : 1994
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 43.1500 - 4.4400 0.97 3861 150 0.1684 0.1888
REMARK 3 2 4.4400 - 3.5200 1.00 3803 148 0.1584 0.1876
REMARK 3 3 3.5200 - 3.0800 1.00 3791 147 0.1829 0.2817
REMARK 3 4 3.0800 - 2.8000 0.99 3695 144 0.2119 0.2634
REMARK 3 5 2.8000 - 2.5900 0.98 3673 143 0.2125 0.3016
REMARK 3 6 2.5900 - 2.4400 0.98 3655 141 0.2098 0.3022
REMARK 3 7 2.4400 - 2.3200 0.98 3666 143 0.2069 0.2732
REMARK 3 8 2.3200 - 2.2200 0.98 3686 143 0.2253 0.2716
REMARK 3 9 2.2200 - 2.1300 0.99 3679 142 0.2111 0.3070
REMARK 3 10 2.1300 - 2.0600 0.99 3692 143 0.2243 0.2906
REMARK 3 11 2.0600 - 2.0000 1.00 3721 145 0.2435 0.3038
REMARK 3 12 2.0000 - 1.9400 0.99 3653 142 0.2602 0.3169
REMARK 3 13 1.9400 - 1.8900 0.96 3543 138 0.2941 0.3717
REMARK 3 14 1.8900 - 1.8400 0.87 3232 125 0.3121 0.3305
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) : 0.232
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.172
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 29.86
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.75
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 4894
REMARK 3 ANGLE : 0.745 6644
REMARK 3 CHIRALITY : 0.051 782
REMARK 3 PLANARITY : 0.005 861
REMARK 3 DIHEDRAL : 5.105 3516
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 12
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 99 )
REMARK 3 ORIGIN FOR THE GROUP (A): -6.2426 -23.0159 -28.6306
REMARK 3 T TENSOR
REMARK 3 T11: 0.4159 T22: 0.3435
REMARK 3 T33: 0.2784 T12: 0.0223
REMARK 3 T13: -0.0454 T23: -0.0062
REMARK 3 L TENSOR
REMARK 3 L11: 2.7779 L22: 3.0692
REMARK 3 L33: 2.1144 L12: -0.6227
REMARK 3 L13: -0.3261 L23: -0.2513
REMARK 3 S TENSOR
REMARK 3 S11: 0.1460 S12: 0.0810 S13: -0.1988
REMARK 3 S21: -0.2447 S22: -0.0699 S23: -0.1968
REMARK 3 S31: 0.3906 S32: 0.1322 S33: -0.0877
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 100 THROUGH 228 )
REMARK 3 ORIGIN FOR THE GROUP (A): -12.4756 -5.0741 -13.3738
REMARK 3 T TENSOR
REMARK 3 T11: 0.2116 T22: 0.3009
REMARK 3 T33: 0.3009 T12: 0.0059
REMARK 3 T13: -0.0071 T23: 0.0259
REMARK 3 L TENSOR
REMARK 3 L11: 0.4951 L22: 3.3396
REMARK 3 L33: 5.6784 L12: -0.0834
REMARK 3 L13: 0.1348 L23: 1.2693
REMARK 3 S TENSOR
REMARK 3 S11: -0.0401 S12: -0.0381 S13: 0.0706
REMARK 3 S21: 0.1169 S22: 0.0334 S23: 0.0377
REMARK 3 S31: -0.1756 S32: 0.0739 S33: -0.0011
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 229 THROUGH 354 )
REMARK 3 ORIGIN FOR THE GROUP (A): -20.0063 -3.0487 -33.2756
REMARK 3 T TENSOR
REMARK 3 T11: 0.2700 T22: 0.2911
REMARK 3 T33: 0.2027 T12: -0.0173
REMARK 3 T13: -0.0511 T23: 0.0331
REMARK 3 L TENSOR
REMARK 3 L11: 1.0575 L22: 6.5096
REMARK 3 L33: 2.1650 L12: -1.0918
REMARK 3 L13: -0.2421 L23: 0.7128
REMARK 3 S TENSOR
REMARK 3 S11: 0.1091 S12: 0.0981 S13: -0.0335
REMARK 3 S21: -0.1987 S22: -0.0829 S23: 0.1115
REMARK 3 S31: 0.1120 S32: -0.0758 S33: -0.0334
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 18 THROUGH 45 )
REMARK 3 ORIGIN FOR THE GROUP (A): -37.4331 -25.5759 -5.9371
REMARK 3 T TENSOR
REMARK 3 T11: 0.2003 T22: 0.3307
REMARK 3 T33: 0.3271 T12: -0.0297
REMARK 3 T13: -0.0298 T23: 0.0409
REMARK 3 L TENSOR
REMARK 3 L11: 5.3950 L22: 7.5051
REMARK 3 L33: 7.5143 L12: 1.2731
REMARK 3 L13: 1.4585 L23: 2.3226
REMARK 3 S TENSOR
REMARK 3 S11: -0.1310 S12: -0.0463 S13: -0.1085
REMARK 3 S21: 0.0157 S22: 0.2328 S23: -0.7259
REMARK 3 S31: -0.2256 S32: 0.6884 S33: -0.0902
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 46 THROUGH 86 )
REMARK 3 ORIGIN FOR THE GROUP (A): -31.8582 -23.2877 -10.8971
REMARK 3 T TENSOR
REMARK 3 T11: 0.3401 T22: 0.3745
REMARK 3 T33: 0.3963 T12: 0.0534
REMARK 3 T13: 0.0605 T23: -0.0591
REMARK 3 L TENSOR
REMARK 3 L11: 9.1033 L22: 6.8370
REMARK 3 L33: 3.3897 L12: 5.9676
REMARK 3 L13: 1.3802 L23: -0.9654
REMARK 3 S TENSOR
REMARK 3 S11: 0.0622 S12: -0.3087 S13: -0.0356
REMARK 3 S21: -0.3469 S22: -0.2620 S23: -0.6223
REMARK 3 S31: -0.1960 S32: 0.3059 S33: 0.1600
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 87 THROUGH 120 )
REMARK 3 ORIGIN FOR THE GROUP (A): -38.4787 -14.0810 -11.1636
REMARK 3 T TENSOR
REMARK 3 T11: 0.3185 T22: 0.3325
REMARK 3 T33: 0.3296 T12: -0.0795
REMARK 3 T13: -0.0448 T23: 0.0148
REMARK 3 L TENSOR
REMARK 3 L11: 2.9902 L22: 7.1372
REMARK 3 L33: 4.5426 L12: -2.6614
REMARK 3 L13: -1.1374 L23: 2.2649
REMARK 3 S TENSOR
REMARK 3 S11: -0.1454 S12: 0.0361 S13: 0.1581
REMARK 3 S21: -0.4272 S22: 0.3546 S23: -0.4266
REMARK 3 S31: -0.1399 S32: 0.3757 S33: -0.2064
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 121 THROUGH 157 )
REMARK 3 ORIGIN FOR THE GROUP (A): -45.3168 1.5054 12.3140
REMARK 3 T TENSOR
REMARK 3 T11: 0.7655 T22: 0.3367
REMARK 3 T33: 0.3987 T12: 0.0202
REMARK 3 T13: 0.0046 T23: -0.0377
REMARK 3 L TENSOR
REMARK 3 L11: 5.7713 L22: 4.1830
REMARK 3 L33: 7.6964 L12: 1.2510
REMARK 3 L13: -0.5476 L23: 0.2920
REMARK 3 S TENSOR
REMARK 3 S11: -0.1830 S12: -0.5151 S13: 0.4377
REMARK 3 S21: 1.2098 S22: -0.0542 S23: 0.4511
REMARK 3 S31: -0.2886 S32: 0.2632 S33: 0.2277
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 158 THROUGH 184 )
REMARK 3 ORIGIN FOR THE GROUP (A): -37.8609 -2.0432 14.2295
REMARK 3 T TENSOR
REMARK 3 T11: 0.7054 T22: 0.5323
REMARK 3 T33: 0.5377 T12: 0.0377
REMARK 3 T13: -0.1684 T23: -0.1355
REMARK 3 L TENSOR
REMARK 3 L11: 7.4926 L22: 9.0162
REMARK 3 L33: 5.5734 L12: -2.4702
REMARK 3 L13: -0.9025 L23: 2.2310
REMARK 3 S TENSOR
REMARK 3 S11: -0.0745 S12: -0.7826 S13: 0.3091
REMARK 3 S21: 1.1364 S22: 0.6524 S23: -1.2363
REMARK 3 S31: -0.1935 S32: 0.5462 S33: -0.5422
REMARK 3 TLS GROUP : 9
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 185 THROUGH 206 )
REMARK 3 ORIGIN FOR THE GROUP (A): -46.2753 -10.9470 8.6667
REMARK 3 T TENSOR
REMARK 3 T11: 0.4338 T22: 0.3121
REMARK 3 T33: 0.3458 T12: -0.0406
REMARK 3 T13: 0.0087 T23: -0.0175
REMARK 3 L TENSOR
REMARK 3 L11: 4.5231 L22: 2.3039
REMARK 3 L33: 5.9181 L12: -2.8017
REMARK 3 L13: -0.5626 L23: 2.1282
REMARK 3 S TENSOR
REMARK 3 S11: -0.2164 S12: -0.2718 S13: 0.0121
REMARK 3 S21: 0.6667 S22: -0.0708 S23: 0.6902
REMARK 3 S31: 0.0450 S32: -0.1852 S33: 0.2489
REMARK 3 TLS GROUP : 10
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 207 THROUGH 256 )
REMARK 3 ORIGIN FOR THE GROUP (A): -45.3002 -10.5925 -12.1819
REMARK 3 T TENSOR
REMARK 3 T11: 0.3090 T22: 0.3088
REMARK 3 T33: 0.2984 T12: -0.0465
REMARK 3 T13: -0.0874 T23: 0.0484
REMARK 3 L TENSOR
REMARK 3 L11: 1.6626 L22: 7.2333
REMARK 3 L33: 1.3060 L12: -1.4625
REMARK 3 L13: 0.2377 L23: 1.5209
REMARK 3 S TENSOR
REMARK 3 S11: -0.1299 S12: 0.1256 S13: 0.0268
REMARK 3 S21: -0.4015 S22: 0.0316 S23: 0.2961
REMARK 3 S31: -0.2532 S32: 0.0381 S33: 0.1156
REMARK 3 TLS GROUP : 11
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 257 THROUGH 298 )
REMARK 3 ORIGIN FOR THE GROUP (A): -49.5921 3.8068 -7.8958
REMARK 3 T TENSOR
REMARK 3 T11: 0.4275 T22: 0.2873
REMARK 3 T33: 0.3580 T12: 0.0220
REMARK 3 T13: -0.0514 T23: 0.0582
REMARK 3 L TENSOR
REMARK 3 L11: 6.1107 L22: 6.6423
REMARK 3 L33: 5.7689 L12: 1.8040
REMARK 3 L13: 2.9930 L23: 1.6104
REMARK 3 S TENSOR
REMARK 3 S11: -0.1577 S12: 0.1236 S13: 0.3522
REMARK 3 S21: -0.2961 S22: -0.0831 S23: 0.5102
REMARK 3 S31: -0.5401 S32: -0.1232 S33: 0.2726
REMARK 3 TLS GROUP : 12
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 299 THROUGH 357 )
REMARK 3 ORIGIN FOR THE GROUP (A): -45.4550 0.5214 -16.8692
REMARK 3 T TENSOR
REMARK 3 T11: 0.4907 T22: 0.3755
REMARK 3 T33: 0.4018 T12: -0.0346
REMARK 3 T13: -0.1402 T23: 0.1048
REMARK 3 L TENSOR
REMARK 3 L11: 1.1233 L22: 5.9914
REMARK 3 L33: 4.1091 L12: 0.7999
REMARK 3 L13: 0.2289 L23: 3.3207
REMARK 3 S TENSOR
REMARK 3 S11: -0.0782 S12: -0.0030 S13: 0.2066
REMARK 3 S21: -0.6410 S22: -0.0883 S23: 0.0205
REMARK 3 S31: -0.4857 S32: 0.1499 S33: 0.1446
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7CCX 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_1300017398.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-JUN-12
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) : 0.9
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 : 53490
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840
REMARK 200 RESOLUTION RANGE LOW (A) : 43.150
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2
REMARK 200 DATA REDUNDANCY : 4.000
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.07000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7300
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.45200
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.310
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 (%): 37.63
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97
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 35.20550
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.59700
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.40750
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.59700
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.20550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.40750
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 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 SER A 75
REMARK 465 LEU A 76
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 SER C 57
REMARK 465 THR C 58
REMARK 465 THR C 59
REMARK 465 GLY C 60
REMARK 465 ASP C 61
REMARK 465 LYS C 62
REMARK 465 ILE C 63
REMARK 465 LEU C 64
REMARK 465 ASP C 65
REMARK 465 THR C 66
REMARK 465 ALA C 67
REMARK 465 LEU C 68
REMARK 465 SER C 69
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 GLN C 181
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 43 CG CD CE NZ
REMARK 470 GLN A 50 CG CD OE1 NE2
REMARK 470 PHE A 77 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 LYS A 79 CG CD CE NZ
REMARK 470 GLU A 80 CG CD OE1 OE2
REMARK 470 LYS A 227 CG CD CE NZ
REMARK 470 GLN A 229 CG CD OE1 NE2
REMARK 470 GLU A 258 CG CD OE1 OE2
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 PHE C 77 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 GLU C 80 CG CD OE1 OE2
REMARK 470 GLU C 86 CG CD OE1 OE2
REMARK 470 VAL C 130 CG1 CG2
REMARK 470 LYS C 132 CG CD CE NZ
REMARK 470 GLU C 139 CG CD OE1 OE2
REMARK 470 LYS C 140 CG CD CE NZ
REMARK 470 ARG C 167 CG CD NE CZ NH1 NH2
REMARK 470 ASN C 169 CG OD1 ND2
REMARK 470 GLU C 179 CG CD OE1 OE2
REMARK 470 GLN C 180 CG CD OE1 NE2
REMARK 470 ARG C 201 CG CD NE CZ NH1 NH2
REMARK 470 GLN C 229 CG CD OE1 NE2
REMARK 470 LYS C 272 CG CD CE NZ
REMARK 470 GLN C 356 CG CD OE1 NE2
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 ARG A 19 -69.43 -125.68
REMARK 500 CYS A 211 104.12 -162.47
REMARK 500 VAL A 316 48.11 34.01
REMARK 500 CYS C 211 113.27 -160.20
REMARK 500 SER C 262 32.71 -96.17
REMARK 500 ILE C 299 69.98 -113.77
REMARK 500 VAL C 316 45.83 33.87
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 Di-peptide DPM C 401 and CYS C
REMARK 800 261
DBREF 7CCX A 1 361 UNP P08397 HEM3_HUMAN 1 361
DBREF 7CCX 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 DPM C 401 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
HETSYN DPM DIPYRROMETHANE COFACTOR
FORMUL 3 DPM 2(C20 H24 N2 O8)
FORMUL 5 HOH *159(H2 O)
HELIX 1 AA1 SER A 28 TYR A 46 1 19
HELIX 2 AA2 THR A 78 LYS A 87 1 10
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 THR A 133 LEU A 137 5 5
HELIX 6 AA6 SER A 147 PHE A 158 1 12
HELIX 7 AA7 ASN A 169 GLN A 180 1 12
HELIX 8 AA8 THR A 190 MET A 196 1 7
HELIX 9 AA9 TRP A 198 VAL A 202 5 5
HELIX 10 AB1 ASP A 228 GLY A 236 1 9
HELIX 11 AB2 VAL A 237 HIS A 239 5 3
HELIX 12 AB3 ASP A 240 LEU A 257 1 18
HELIX 13 AB4 PRO A 324 LYS A 345 1 22
HELIX 14 AB5 GLY A 346 ALA A 354 1 9
HELIX 15 AB6 SER C 28 TYR C 46 1 19
HELIX 16 AB7 LEU C 76 LYS C 87 1 12
HELIX 17 AB8 LYS C 98 LEU C 100 5 3
HELIX 18 AB9 PRO C 127 VAL C 130 5 4
HELIX 19 AC1 SER C 147 PHE C 158 1 12
HELIX 20 AC2 ASN C 169 GLN C 180 1 12
HELIX 21 AC3 THR C 190 GLY C 197 1 8
HELIX 22 AC4 TRP C 198 VAL C 202 5 5
HELIX 23 AC5 ASP C 228 GLY C 236 1 9
HELIX 24 AC6 VAL C 237 HIS C 239 5 3
HELIX 25 AC7 ASP C 240 LEU C 257 1 18
HELIX 26 AC8 PRO C 324 LYS C 345 1 22
HELIX 27 AC9 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 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 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 GLN C 50 ALA C 55 0
SHEET 2 AA4 5 VAL C 20 THR C 25 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 GLU C 162
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 MET C 295 N LEU C 278
LINK SG CYS A 261 CHA DPM A 401 1555 1555 1.62
LINK SG CYS C 261 CHA DPM C 401 1555 1555 1.61
SITE 1 AC1 19 SER A 96 LYS A 98 ASP A 99 SER A 146
SITE 2 AC1 19 SER A 147 ARG A 149 ARG A 150 ARG A 173
SITE 3 AC1 19 LEU A 188 ALA A 189 ARG A 195 GLN A 217
SITE 4 AC1 19 GLY A 218 CYS A 261 HOH A 511 HOH A 525
SITE 5 AC1 19 HOH A 534 HOH A 561 HOH A 575
SITE 1 AC2 20 SER C 96 LYS C 98 ASP C 99 SER C 146
SITE 2 AC2 20 SER C 147 ARG C 149 ARG C 150 ARG C 173
SITE 3 AC2 20 LEU C 188 ALA C 189 ALA C 214 GLN C 217
SITE 4 AC2 20 GLY C 218 GLY C 260 SER C 262 VAL C 263
SITE 5 AC2 20 HOH C 501 HOH C 507 HOH C 517 HOH C 534
CRYST1 70.411 80.815 109.194 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 0.014202 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012374 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009158 0.00000