HEADER NUCLEAR PROTEIN 05-SEP-24 9DI4 TITLE RMI1-RMI2 BOUND TO CYCLIC PEPTIDE L4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BLM-ASSOCIATED PROTEIN OF 75 KDA,BLAP75,FAAP75; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RECQ-MEDIATED GENOME INSTABILITY PROTEIN 2; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: HRMI2,BLM-ASSOCIATED PROTEIN OF 18 KDA,BLAP18; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: L4 CYCLIC PEPTIDE; COMPND 13 CHAIN: C; COMPND 14 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: RMI1, C9ORF76; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RMI2, C16ORF75; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS NUCLEAR PROTEIN COMPLEX, GENOME STABILITY, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.BYTHELL-DOUGLAS,Y.H.LAU,L.J.ALCOCK,T.GAO,C.DESHPANDE,K.PATEL REVDAT 2 09-JUL-25 9DI4 1 JRNL REVDAT 1 02-JUL-25 9DI4 0 JRNL AUTH L.J.ALCOCK,T.GAO,R.BYTHELL-DOUGLAS,J.GAO,H.KRISHNA SUDHAKAR, JRNL AUTH 2 T.HUANG,R.YOUNG,Q.N.VU,C.DESHPANDE,L.E.WILKINSON-WHITE, JRNL AUTH 3 T.PASSIOURA,H.A.PICKETT,A.J.DEANS,Y.H.LAU JRNL TITL POTENT CYCLIC PEPTIDE INHIBITORS DISRUPT THE FANCM-RMI JRNL TITL 2 INTERACTION. JRNL REF J.MED.CHEM. V. 68 12615 2025 JRNL REFN ISSN 0022-2623 JRNL PMID 40479515 JRNL DOI 10.1021/ACS.JMEDCHEM.5C00365 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.856 REMARK 3 FREE R VALUE TEST SET COUNT : 673 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 929 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3130 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2281 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.40100 REMARK 3 B22 (A**2) : -3.40100 REMARK 3 B33 (A**2) : 11.03300 REMARK 3 B12 (A**2) : -1.70100 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.358 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.286 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.232 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.245 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2327 ; 0.015 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2286 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3150 ; 2.979 ; 1.845 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5281 ; 0.934 ; 1.758 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 7.959 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 18 ;21.000 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;17.726 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 354 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2713 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 499 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 410 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 88 ; 0.151 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1104 ; 0.198 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 42 ; 0.190 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1176 ; 7.644 ; 5.748 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1175 ; 7.636 ; 5.747 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1465 ; 9.794 ;10.301 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1465 ; 9.784 ;10.300 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1151 ;10.732 ; 6.475 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1152 ;10.728 ; 6.475 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1685 ;14.219 ;11.456 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1686 ;14.215 ;11.455 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9DI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000288176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 49.169 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 38.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M ZINC CHLORIDE, 0.1M SODIUM REMARK 280 ACETATE PH 5.0, 20% W/V PEG 6000, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.53600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.07200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.53600 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.07200 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 29.53600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 59.07200 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 29.53600 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 59.07200 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 ZN ZN A 701 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 807 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 103 LIES ON A SPECIAL POSITION. 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 474 REMARK 465 GLU A 475 REMARK 465 ASN A 476 REMARK 465 SER A 477 REMARK 465 ILE A 478 REMARK 465 ASN A 479 REMARK 465 LEU A 480 REMARK 465 SER A 481 REMARK 465 ILE A 482 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 ALA B 5 REMARK 465 ASP B 6 REMARK 465 SER B 7 REMARK 465 PHE B 8 REMARK 465 SER B 9 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 H ASN A 612 HD1 HIS A 615 1.18 REMARK 500 HE2 HIS B 131 O HOH B 301 1.41 REMARK 500 OE2 GLU A 548 O HOH A 801 2.14 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 GLU B 138 CD GLU B 138 OE1 0.085 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 LYS A 509 CD - CE - NZ ANGL. DEV. = -13.9 DEGREES REMARK 500 ASN A 520 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG A 583 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 MET A 592 CG - SD - CE ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG B 31 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 32 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 45 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 50 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 MET B 66 CG - SD - CE ANGL. DEV. = 24.4 DEGREES REMARK 500 ARG B 69 N - CA - CB ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG B 73 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 73 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 75 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 GLU B 87 CG - CD - OE1 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG B 88 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 LEU B 117 CB - CG - CD1 ANGL. DEV. = -11.1 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 ALA B 40 39.71 -141.98 REMARK 500 ALA B 48 30.90 -87.26 REMARK 500 LEU B 55 67.61 -112.69 REMARK 500 ARG B 69 -110.24 82.30 REMARK 500 ASN B 128 95.24 -166.20 REMARK 500 PHE C 5 -107.68 -128.73 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 A 583 0.25 SIDE CHAIN REMARK 500 ARG B 32 0.20 SIDE CHAIN REMARK 500 ARG B 42 0.16 SIDE CHAIN REMARK 500 ARG B 63 0.13 SIDE CHAIN REMARK 500 ARG B 88 0.14 SIDE CHAIN REMARK 500 ARG B 93 0.18 SIDE CHAIN REMARK 500 ARG B 144 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 548 OE2 REMARK 620 2 GLU A 548 OE2 0.0 REMARK 620 3 HOH A 801 O 54.3 54.3 REMARK 620 4 HOH A 801 O 130.6 130.6 173.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 28 OE2 REMARK 620 2 GLU B 114 OE1 54.3 REMARK 620 3 HOH B 313 O 67.9 13.7 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9DHK RELATED DB: PDB REMARK 900 RMI1-RMI2 HETERODIMER BOUND TO THE L3 CYCLIC PEPTIDE DBREF 9DI4 A 475 625 UNP Q9H9A7 RMI1_HUMAN 475 625 DBREF 9DI4 B 1 147 UNP Q96E14 RMI2_HUMAN 1 147 DBREF 9DI4 C 0 14 PDB 9DI4 9DI4 0 14 SEQADV 9DI4 MET A 474 UNP Q9H9A7 INITIATING METHIONINE SEQRES 1 A 152 MET GLU ASN SER ILE ASN LEU SER ILE ALA MET ASP LEU SEQRES 2 A 152 TYR SER PRO PRO PHE VAL TYR LEU SER VAL LEU MET ALA SEQRES 3 A 152 SER LYS PRO LYS GLU VAL THR THR VAL LYS VAL LYS ALA SEQRES 4 A 152 PHE ILE VAL THR LEU THR GLY ASN LEU SER SER SER GLY SEQRES 5 A 152 GLY ILE TRP SER ILE THR ALA LYS VAL SER ASP GLY THR SEQRES 6 A 152 ALA TYR LEU ASP VAL ASP PHE VAL ASP GLU ILE LEU THR SEQRES 7 A 152 SER LEU ILE GLY PHE SER VAL PRO GLU MET LYS GLN SER SEQRES 8 A 152 LYS LYS ASP PRO LEU GLN TYR GLN LYS PHE LEU GLU GLY SEQRES 9 A 152 LEU GLN LYS CYS GLN ARG ASP LEU ILE ASP LEU CYS CYS SEQRES 10 A 152 LEU MET THR ILE SER PHE ASN PRO SER LEU SER LYS ALA SEQRES 11 A 152 MET VAL LEU ALA LEU GLN ASP VAL ASN MET GLU HIS LEU SEQRES 12 A 152 GLU ASN LEU LYS LYS ARG LEU ASN LYS SEQRES 1 B 147 MET ALA ALA ALA ALA ASP SER PHE SER GLY GLY PRO ALA SEQRES 2 B 147 GLY VAL ARG LEU PRO ARG SER PRO PRO LEU LYS VAL LEU SEQRES 3 B 147 ALA GLU GLN LEU ARG ARG ASP ALA GLU GLY GLY PRO GLY SEQRES 4 B 147 ALA TRP ARG LEU SER ARG ALA ALA ALA GLY ARG GLY PRO SEQRES 5 B 147 LEU ASP LEU ALA ALA VAL TRP MET GLN GLY ARG VAL VAL SEQRES 6 B 147 MET ALA ASP ARG GLY GLU ALA ARG LEU ARG ASP PRO SER SEQRES 7 B 147 GLY ASP PHE SER VAL ARG GLY LEU GLU ARG VAL PRO ARG SEQRES 8 B 147 GLY ARG PRO CYS LEU VAL PRO GLY LYS TYR VAL MET VAL SEQRES 9 B 147 MET GLY VAL VAL GLN ALA CYS SER PRO GLU PRO CYS LEU SEQRES 10 B 147 GLN ALA VAL LYS MET THR ASP LEU SER ASP ASN PRO ILE SEQRES 11 B 147 HIS GLU SER MET TRP GLU LEU GLU VAL GLU ASP LEU HIS SEQRES 12 B 147 ARG ASN ILE PRO SEQRES 1 C 15 ACE TYR SER ILE LEU PHE ASP LYS TYR TYR SER ILE PRO SEQRES 2 C 15 CYS NH2 HET ACE C 0 5 HET NH2 C 14 3 HET ZN A 701 1 HET ZN B 201 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 3 ACE C2 H4 O FORMUL 3 NH2 H2 N FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *38(H2 O) HELIX 1 AA1 TYR A 493 SER A 500 1 8 HELIX 2 AA2 SER A 523 ILE A 527 5 5 HELIX 3 AA3 VAL A 546 GLY A 555 1 10 HELIX 4 AA4 SER A 557 LYS A 565 1 9 HELIX 5 AA5 ASP A 567 LEU A 588 1 22 HELIX 6 AA6 ASN A 612 LEU A 623 1 12 HELIX 7 AA7 LEU B 26 ASP B 33 1 8 HELIX 8 AA8 PRO B 129 ASN B 145 1 17 SHEET 1 AA1 6 THR A 506 LEU A 517 0 SHEET 2 AA1 6 THR A 531 SER A 535 -1 O LYS A 533 N THR A 516 SHEET 3 AA1 6 TYR A 540 PHE A 545 -1 O VAL A 543 N ALA A 532 SHEET 4 AA1 6 LYS A 602 GLN A 609 1 O VAL A 605 N ASP A 544 SHEET 5 AA1 6 CYS A 589 ASN A 597 -1 N THR A 593 O LEU A 606 SHEET 6 AA1 6 THR A 506 LEU A 517 -1 N VAL A 510 O MET A 592 SHEET 1 AA2 7 LEU B 23 LYS B 24 0 SHEET 2 AA2 7 ALA B 57 ASP B 68 1 O TRP B 59 N LEU B 23 SHEET 3 AA2 7 TYR B 101 ALA B 110 -1 O VAL B 104 N MET B 60 SHEET 4 AA2 7 CYS B 116 ASP B 124 -1 O CYS B 116 N GLN B 109 SHEET 5 AA2 7 GLY B 79 ARG B 84 1 N ARG B 84 O LEU B 117 SHEET 6 AA2 7 GLU B 71 ASP B 76 -1 N LEU B 74 O PHE B 81 SHEET 7 AA2 7 ALA B 57 ASP B 68 -1 N VAL B 65 O ARG B 73 SHEET 1 AA3 3 ALA B 34 GLU B 35 0 SHEET 2 AA3 3 ARG B 42 LEU B 43 -1 O ARG B 42 N GLU B 35 SHEET 3 AA3 3 LEU B 53 ASP B 54 -1 O LEU B 53 N LEU B 43 SHEET 1 AA4 2 TYR C 1 LEU C 4 0 SHEET 2 AA4 2 TYR C 8 ILE C 11 -1 O ILE C 11 N TYR C 1 LINK C ACE C 0 N TYR C 1 1555 1555 1.30 LINK CH3 ACE C 0 SG CYS C 13 1555 1555 1.80 LINK C CYS C 13 N NH2 C 14 1555 1555 1.31 LINK OE2 GLU A 548 ZN ZN A 701 1555 1555 2.27 LINK OE2 GLU A 548 ZN ZN A 701 1555 7555 2.27 LINK ZN ZN A 701 O HOH A 801 1555 1555 2.41 LINK ZN ZN A 701 O HOH A 801 1555 7555 2.41 LINK OE2 GLU B 28 ZN ZN B 201 1555 4445 2.07 LINK OE1 GLU B 114 ZN ZN B 201 1555 1555 2.17 LINK ZN ZN B 201 O HOH B 313 1555 1555 2.65 CISPEP 1 PRO A 489 PRO A 490 0 1.38 CISPEP 2 SER B 112 PRO B 113 0 -8.09 CRYST1 136.298 136.298 88.608 90.00 90.00 120.00 P 64 2 2 12 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 0.007337 0.004236 0.000000 0.00000 SCALE2 0.000000 0.008472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011286 0.00000 CONECT 996 4619 CONECT 3854 4620 CONECT 4390 4391 4392 4395 CONECT 4391 4390 CONECT 4392 4390 4393 4394 4610 CONECT 4393 4392 CONECT 4394 4392 CONECT 4395 4390 CONECT 4607 4615 CONECT 4610 4392 CONECT 4615 4607 4616 4617 CONECT 4616 4615 CONECT 4617 4615 CONECT 4619 996 4621 CONECT 4620 3854 4648 CONECT 4621 4619 CONECT 4648 4620 MASTER 442 0 4 8 18 0 0 6 2321 3 17 26 END