HEADER RNA BINDING PROTEIN 10-MAR-25 9M7M TITLE CRYSTAL STRUCTURE OF HUMAN PSEUDOURIDINE 5'-MONOPHOSPHATE PHOSPHATASE TITLE 2 (HHDHD1A) COMPLEXED WITH PSEUDOURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOURIDINE-5'-PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING COMPND 5 PROTEIN 1,HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING COMPND 6 PROTEIN 1A,PROTEIN GS1,PSEUDOURIDINE-5'-MONOPHOSPHATASE,5'-PSIMPASE; COMPND 7 EC: 3.1.3.96; COMPND 8 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: PUDP, DXF68S1E, FAM16AX, GS1, HDHD1, HDHD1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PSEUDOURIDINE MONOPHOSPHATE PHOSPHATASE, HAD PHOSPHATASE, COFACTOR, KEYWDS 2 PSEUDOURIDINE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SEO,S.RHEE REVDAT 2 02-JUL-25 9M7M 1 JRNL REVDAT 1 18-JUN-25 9M7M 0 JRNL AUTH S.SEO,M.KIM,S.RHEE JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE SUBSTRATE JRNL TITL 2 SPECIFICITY OF THE PSEUDOURIDINE MONOPHOSPHATE PHOSPHATASE JRNL TITL 3 HDHD1A. JRNL REF J.BIOL.CHEM. V. 301 10257 2025 JRNL REFN ESSN 1083-351X JRNL PMID 40409548 JRNL DOI 10.1016/J.JBC.2025.110257 REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 107923 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.550 REMARK 3 FREE R VALUE TEST SET COUNT : 3836 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 29.7920 - 3.7777 0.99 4007 145 0.1391 0.1505 REMARK 3 2 3.7777 - 2.9994 1.00 4027 149 0.1527 0.1728 REMARK 3 3 2.9994 - 2.6205 1.00 4009 152 0.1705 0.1804 REMARK 3 4 2.6205 - 2.3810 0.99 3992 149 0.1588 0.1751 REMARK 3 5 2.3810 - 2.2104 0.99 4001 148 0.1616 0.2158 REMARK 3 6 2.2104 - 2.0801 0.99 3958 144 0.1684 0.2115 REMARK 3 7 2.0801 - 1.9760 0.98 3929 143 0.1776 0.2362 REMARK 3 8 1.9760 - 1.8900 0.97 3902 145 0.1775 0.2024 REMARK 3 9 1.8900 - 1.8172 0.97 3871 143 0.1839 0.2063 REMARK 3 10 1.8172 - 1.7545 0.95 3882 145 0.1944 0.2019 REMARK 3 11 1.7545 - 1.6997 0.94 3777 138 0.2094 0.2683 REMARK 3 12 1.6997 - 1.6511 0.94 3795 139 0.2180 0.2548 REMARK 3 13 1.6511 - 1.6076 0.94 3748 135 0.2293 0.2863 REMARK 3 14 1.6076 - 1.5684 0.94 3759 139 0.2165 0.2354 REMARK 3 15 1.5684 - 1.5328 0.94 3859 143 0.2235 0.2292 REMARK 3 16 1.5328 - 1.5001 0.93 3714 138 0.2340 0.2477 REMARK 3 17 1.5001 - 1.4701 0.94 3825 144 0.2362 0.2796 REMARK 3 18 1.4701 - 1.4424 0.95 3762 139 0.2534 0.2691 REMARK 3 19 1.4424 - 1.4166 0.95 3821 142 0.2533 0.2624 REMARK 3 20 1.4166 - 1.3926 0.96 3854 140 0.2714 0.2566 REMARK 3 21 1.3926 - 1.3702 0.95 3798 141 0.2691 0.3694 REMARK 3 22 1.3702 - 1.3491 0.95 3780 136 0.2701 0.2852 REMARK 3 23 1.3491 - 1.3292 0.96 3851 140 0.2726 0.2919 REMARK 3 24 1.3292 - 1.3105 0.95 3817 139 0.2832 0.3045 REMARK 3 25 1.3105 - 1.2928 0.95 3834 143 0.2916 0.3221 REMARK 3 26 1.2928 - 1.2760 0.94 3759 139 0.2895 0.3269 REMARK 3 27 1.2760 - 1.2601 0.93 3756 138 0.3008 0.3347 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.016 1819 REMARK 3 ANGLE : 1.551 2470 REMARK 3 CHIRALITY : 0.096 282 REMARK 3 PLANARITY : 0.010 318 REMARK 3 DIHEDRAL : 11.635 675 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 24.0030 16.0201 11.5378 REMARK 3 T TENSOR REMARK 3 T11: 0.0569 T22: 0.0295 REMARK 3 T33: 0.0570 T12: -0.0169 REMARK 3 T13: -0.0135 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.7028 L22: 0.4852 REMARK 3 L33: 1.4542 L12: 0.0117 REMARK 3 L13: 0.6489 L23: 0.1282 REMARK 3 S TENSOR REMARK 3 S11: 0.0752 S12: -0.0937 S13: -0.0587 REMARK 3 S21: 0.0475 S22: -0.0180 S23: -0.0281 REMARK 3 S31: 0.0783 S32: -0.0235 S33: 0.0301 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 9M7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS V20230630 REMARK 200 DATA SCALING SOFTWARE : XDS V20230630 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107923 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 12.53 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M TRIS REMARK 280 -HCL (PH 8.5), 30% (W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.12500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.54500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.12500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 409 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 615 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 618 LIES ON A SPECIAL POSITION. 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 201 NE CZ NH1 NH2 REMARK 470 GLU A 228 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 O HOH A 555 O HOH A 556 2.00 REMARK 500 O HOH A 403 O HOH A 462 2.02 REMARK 500 OE1 GLN A 66 O HOH A 401 2.02 REMARK 500 O HOH A 576 O HOH A 646 2.04 REMARK 500 O HOH A 638 O HOH A 683 2.04 REMARK 500 O HOH A 446 O HOH A 612 2.04 REMARK 500 O HOH A 691 O HOH A 700 2.07 REMARK 500 O HOH A 489 O HOH A 595 2.07 REMARK 500 O HOH A 404 O HOH A 619 2.07 REMARK 500 O HOH A 589 O HOH A 610 2.10 REMARK 500 O HOH A 653 O HOH A 694 2.10 REMARK 500 O HOH A 403 O HOH A 581 2.10 REMARK 500 O HOH A 412 O HOH A 611 2.12 REMARK 500 O HOH A 575 O HOH A 678 2.12 REMARK 500 O HOH A 587 O HOH A 597 2.16 REMARK 500 O HOH A 478 O HOH A 513 2.16 REMARK 500 N ALA A 3 O HOH A 402 2.16 REMARK 500 O HOH A 437 O HOH A 548 2.16 REMARK 500 OD1 ASP A 153 O HOH A 403 2.16 REMARK 500 O HOH A 421 O HOH A 583 2.17 REMARK 500 O HOH A 563 O HOH A 680 2.18 REMARK 500 O HOH A 422 O HOH A 636 2.18 REMARK 500 O HOH A 440 O HOH A 568 2.18 REMARK 500 O HOH A 431 O HOH A 670 2.19 REMARK 500 O HOH A 416 O HOH A 567 2.19 REMARK 500 O HOH A 410 O HOH A 425 2.19 REMARK 500 O HOH A 417 O HOH A 654 2.19 REMARK 500 O HOH A 410 O HOH A 413 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 A 661 O HOH A 690 3645 2.14 REMARK 500 O HOH A 646 O HOH A 692 2565 2.18 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 MET A 50 CG - SD - CE ANGL. DEV. = -12.8 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 MET A 15 -67.81 -105.04 REMARK 500 ASP A 21 49.12 -84.86 REMARK 500 PRO A 68 46.83 -87.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 695 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 696 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 697 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 698 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A 699 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A 700 DISTANCE = 6.89 ANGSTROMS 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 14 OD2 REMARK 620 2 ASP A 16 O 88.8 REMARK 620 3 ASP A 176 OD1 88.7 91.5 REMARK 620 4 HOH A 426 O 88.0 173.7 93.7 REMARK 620 5 HOH A 429 O 171.9 87.8 84.1 96.1 REMARK 620 6 HOH A 511 O 99.8 94.0 170.0 81.2 87.8 REMARK 620 N 1 2 3 4 5 DBREF 9M7M A 3 228 UNP Q08623 HDHD1_HUMAN 3 228 SEQRES 1 A 226 ALA PRO PRO GLN PRO VAL THR HIS LEU ILE PHE ASP MET SEQRES 2 A 226 ASP GLY LEU LEU LEU ASP THR GLU ARG LEU TYR SER VAL SEQRES 3 A 226 VAL PHE GLN GLU ILE CYS ASN ARG TYR ASP LYS LYS TYR SEQRES 4 A 226 SER TRP ASP VAL LYS SER LEU VAL MET GLY LYS LYS ALA SEQRES 5 A 226 LEU GLU ALA ALA GLN ILE ILE ILE ASP VAL LEU GLN LEU SEQRES 6 A 226 PRO MET SER LYS GLU GLU LEU VAL GLU GLU SER GLN THR SEQRES 7 A 226 LYS LEU LYS GLU VAL PHE PRO THR ALA ALA LEU MET PRO SEQRES 8 A 226 GLY ALA GLU LYS LEU ILE ILE HIS LEU ARG LYS HIS GLY SEQRES 9 A 226 ILE PRO PHE ALA LEU ALA THR SER SER GLY SER ALA SER SEQRES 10 A 226 PHE ASP MET LYS THR SER ARG HIS LYS GLU PHE PHE SER SEQRES 11 A 226 LEU PHE SER HIS ILE VAL LEU GLY ASP ASP PRO GLU VAL SEQRES 12 A 226 GLN HIS GLY LYS PRO ASP PRO ASP ILE PHE LEU ALA CYS SEQRES 13 A 226 ALA LYS ARG PHE SER PRO PRO PRO ALA MET GLU LYS CYS SEQRES 14 A 226 LEU VAL PHE GLU ASP ALA PRO ASN GLY VAL GLU ALA ALA SEQRES 15 A 226 LEU ALA ALA GLY MET GLN VAL VAL MET VAL PRO ASP GLY SEQRES 16 A 226 ASN LEU SER ARG ASP LEU THR THR LYS ALA THR LEU VAL SEQRES 17 A 226 LEU ASN SER LEU GLN ASP PHE GLN PRO GLU LEU PHE GLY SEQRES 18 A 226 LEU PRO SER TYR GLU HET MG A 301 1 HET FJF A 302 17 HETNAM MG MAGNESIUM ION HETNAM FJF 5-[(2~{S},3~{R},4~{S},5~{R})-5-(HYDROXYMETHYL)-3,4- HETNAM 2 FJF BIS(OXIDANYL)OXOLAN-2-YL]-1~{H}-PYRIMIDINE-2,4-DIONE FORMUL 2 MG MG 2+ FORMUL 3 FJF C9 H12 N2 O6 FORMUL 4 HOH *300(H2 O) HELIX 1 AA1 THR A 22 ARG A 36 1 15 HELIX 2 AA2 SER A 42 MET A 50 1 9 HELIX 3 AA3 LYS A 53 GLN A 66 1 14 HELIX 4 AA4 SER A 70 LYS A 83 1 14 HELIX 5 AA5 GLU A 84 ALA A 89 5 6 HELIX 6 AA6 GLY A 94 HIS A 105 1 12 HELIX 7 AA7 GLY A 116 SER A 125 1 10 HELIX 8 AA8 HIS A 127 SER A 132 1 6 HELIX 9 AA9 PRO A 152 LYS A 160 1 9 HELIX 10 AB1 ALA A 167 GLU A 169 5 3 HELIX 11 AB2 ALA A 177 ALA A 187 1 11 HELIX 12 AB3 ARG A 201 THR A 205 5 5 HELIX 13 AB4 SER A 213 PHE A 217 5 5 HELIX 14 AB5 GLN A 218 GLY A 223 5 6 SHEET 1 AA1 6 ILE A 137 VAL A 138 0 SHEET 2 AA1 6 PHE A 109 ALA A 112 1 N LEU A 111 O VAL A 138 SHEET 3 AA1 6 HIS A 10 PHE A 13 1 N PHE A 13 O ALA A 110 SHEET 4 AA1 6 CYS A 171 GLU A 175 1 O LEU A 172 N ILE A 12 SHEET 5 AA1 6 GLN A 190 MET A 193 1 O VAL A 192 N VAL A 173 SHEET 6 AA1 6 LEU A 209 VAL A 210 1 O LEU A 209 N MET A 193 LINK OD2 ASP A 14 MG MG A 301 1555 1555 1.99 LINK O ASP A 16 MG MG A 301 1555 1555 2.10 LINK OD1 ASP A 176 MG MG A 301 1555 1555 2.09 LINK MG MG A 301 O HOH A 426 1555 1555 2.11 LINK MG MG A 301 O HOH A 429 1555 1555 2.16 LINK MG MG A 301 O HOH A 511 1555 1555 2.07 CISPEP 1 LYS A 149 PRO A 150 0 17.66 CISPEP 2 SER A 163 PRO A 164 0 -3.17 CRYST1 51.620 61.090 68.250 90.00 90.00 90.00 P 2 21 21 4 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 0.019372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014652 0.00000 CONECT 181 3526 CONECT 206 3526 CONECT 2772 3526 CONECT 3526 181 206 2772 3569 CONECT 3526 3572 3654 CONECT 3527 3528 CONECT 3528 3527 3529 3534 CONECT 3529 3528 3530 CONECT 3530 3529 3531 CONECT 3531 3530 3532 3535 CONECT 3532 3531 3533 3534 CONECT 3533 3532 CONECT 3534 3528 3532 CONECT 3535 3531 3536 3542 CONECT 3536 3535 3537 CONECT 3537 3536 3538 3540 CONECT 3538 3537 3539 CONECT 3539 3538 CONECT 3540 3537 3541 3542 CONECT 3541 3540 CONECT 3542 3535 3540 3543 CONECT 3543 3542 CONECT 3569 3526 CONECT 3572 3526 CONECT 3654 3526 MASTER 381 0 2 14 6 0 0 6 2069 1 25 18 END