HEADER TRANSFERASE 06-SEP-24 9JGD TITLE CRYSTAL STRUCTURE OF NEP1 IN COMPLEX WITH 5'-METHYLTHIOADENOSINE FROM TITLE 2 PYROCOCCUS HORIKOSHII OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE NEP1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 16S RRNA (PSEUDOURIDINE-N1-)-METHYLTRANSFERASE NEP1; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII OT3; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 GENE: NEP1, PH1379; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CONSERVED ARGININE RESIDUES, GLOBULAR LOOP EXTENSION, INTER-SUBUNIT KEYWDS 2 INTERACTIONS, NEP1, N1-PSEUDOURIDINE METHYLTRANSFERASE, TREFOIL KEYWDS 3 KNOT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SAHA,S.P.KANAUJIA REVDAT 2 21-MAY-25 9JGD 1 JRNL REVDAT 1 12-MAR-25 9JGD 0 JRNL AUTH S.SAHA,S.P.KANAUJIA JRNL TITL STRUCTURAL ANALYSIS OF THE RIBOSOME ASSEMBLY FACTOR NEP1, AN JRNL TITL 2 N1-SPECIFIC PSEUDOURIDINE METHYLTRANSFERASE, REVEALS JRNL TITL 3 MECHANISTIC INSIGHTS. JRNL REF FEBS J. V. 292 2338 2025 JRNL REFN ISSN 1742-464X JRNL PMID 39918246 JRNL DOI 10.1111/FEBS.70005 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 12283 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 669 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.5380 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.5700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1871 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.32000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : 4.29000 REMARK 3 B12 (A**2) : -0.66000 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): 0.285 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.226 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.044 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 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): 1949 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1932 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2626 ; 1.532 ; 1.668 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4459 ; 0.524 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 225 ; 6.910 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 16 ; 9.936 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 371 ;16.253 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 292 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2202 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 419 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 904 ; 2.596 ; 2.609 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 903 ; 2.590 ; 2.604 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1127 ; 4.016 ; 4.663 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1128 ; 4.016 ; 4.667 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1045 ; 3.768 ; 3.213 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1046 ; 3.767 ; 3.217 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1500 ; 6.029 ; 5.613 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2207 ; 9.016 ;26.600 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2193 ; 9.021 ;26.550 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 227 REMARK 3 ORIGIN FOR THE GROUP (A): -16.4452 12.2807 -32.5755 REMARK 3 T TENSOR REMARK 3 T11: 0.0215 T22: 0.0300 REMARK 3 T33: 0.0610 T12: 0.0187 REMARK 3 T13: 0.0076 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 2.4904 L22: 2.0369 REMARK 3 L33: 0.5863 L12: -0.5618 REMARK 3 L13: -0.1161 L23: 0.2051 REMARK 3 S TENSOR REMARK 3 S11: -0.0642 S12: -0.0157 S13: 0.0728 REMARK 3 S21: 0.0734 S22: 0.0822 S23: -0.0807 REMARK 3 S31: 0.0255 S32: 0.0359 S33: -0.0180 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9JGD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1300051277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13053 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 70.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 0.55200 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 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: TRIGONAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 2.0 REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 56.62000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.68957 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.27333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 56.62000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 32.68957 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.27333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 56.62000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 32.68957 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.27333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 56.62000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 32.68957 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.27333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 56.62000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 32.68957 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.27333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 56.62000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 32.68957 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 34.27333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 65.37914 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 68.54667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 65.37914 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 68.54667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 65.37914 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 68.54667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 65.37914 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 68.54667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 65.37914 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 68.54667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 65.37914 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 68.54667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 -56.62000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 32.68957 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -68.54667 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 468 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 474 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 1 REMARK 465 LYS A 228 REMARK 465 SER A 229 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 451 O HOH A 453 2.14 REMARK 500 O HOH A 470 O HOH A 475 2.15 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 416 O HOH A 416 2555 1.68 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 LYS A 139 140.89 -175.63 REMARK 500 LYS A 177 57.29 -149.41 REMARK 500 TYR A 202 149.56 178.06 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 65 0.09 SIDE CHAIN REMARK 500 ARG A 94 0.12 SIDE CHAIN REMARK 500 ARG A 109 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9JGD A 1 229 UNP O50087 NEP1_PYRHO 1 229 SEQRES 1 A 229 MET GLU GLU LYS LYS ARG LEU HIS LEU ILE ILE ALA ASP SEQRES 2 A 229 ALA GLU LEU GLU THR VAL PRO PRO GLU ILE LEU ASP HIS SEQRES 3 A 229 PRO ALA ILE VAL ASN TYR ALA LYS ARG ARG LYS LYS ARG SEQRES 4 A 229 PRO GLU LYS ILE ILE LEU ASP SER THR TYR HIS HIS ALA SEQRES 5 A 229 ALA LEU ARG GLN LEU GLU ASP GLY GLU ARG ARG GLY ARG SEQRES 6 A 229 PRO ASP ILE VAL HIS ILE CYS LEU LEU ASN ALA LEU ASP SEQRES 7 A 229 SER ILE LEU ASN LYS GLU ASP ARG LEU ARG VAL TYR VAL SEQRES 8 A 229 HIS THR ARG ASN ASP TYR VAL ILE TYR ILE LYS PRO GLU SEQRES 9 A 229 THR ARG LEU PRO ARG ASN TYR ASN ARG PHE ILE GLY LEU SEQRES 10 A 229 MET GLU ASN LEU PHE GLU LYS GLY ALA VAL PRO GLU ASP SEQRES 11 A 229 LEU GLU LEU LEU ARG MET GLU LYS LYS THR LEU ASN GLU SEQRES 12 A 229 LEU ILE GLU GLU ILE ASN PRO ASP VAL VAL PHE ILE MET SEQRES 13 A 229 HIS GLU GLU GLY GLU LEU MET ILE PRO LYS ASN PHE GLY SEQRES 14 A 229 LYS LEU LEU ASP LYS PHE LYS LYS PRO THR VAL ILE VAL SEQRES 15 A 229 GLY GLY PHE PRO HIS GLY ASP PHE LYS SER LYS VAL ASP SEQRES 16 A 229 GLY VAL LYS ILE SER LEU TYR ARG GLU PRO LEU MET ALA SEQRES 17 A 229 TRP THR ILE VAL ASN GLU VAL ILE VAL SER TYR GLU TRP SEQRES 18 A 229 GLU VAL ILE LYS LYS PHE LYS SER HET CL A 301 1 HET MTA A 302 20 HET EDO A 303 4 HET GOL A 304 6 HET GOL A 305 6 HET ACT A 306 4 HETNAM CL CHLORIDE ION HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CL CL 1- FORMUL 3 MTA C11 H15 N5 O3 S FORMUL 4 EDO C2 H6 O2 FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 ACT C2 H3 O2 1- FORMUL 8 HOH *90(H2 O) HELIX 1 AA1 PRO A 20 LEU A 24 5 5 HELIX 2 AA2 HIS A 26 ARG A 36 1 11 HELIX 3 AA3 ARG A 39 ILE A 43 5 5 HELIX 4 AA4 ASP A 46 HIS A 51 1 6 HELIX 5 AA5 ALA A 52 LEU A 54 5 3 HELIX 6 AA6 ASP A 59 ARG A 63 5 5 HELIX 7 AA7 ARG A 65 ASP A 78 1 14 HELIX 8 AA8 SER A 79 GLU A 84 1 6 HELIX 9 AA9 ASN A 110 GLY A 125 1 16 HELIX 10 AB1 THR A 140 ASN A 149 1 10 HELIX 11 AB2 ILE A 164 ASP A 173 1 10 HELIX 12 AB3 MET A 207 ILE A 224 1 18 SHEET 1 AA1 9 ALA A 126 VAL A 127 0 SHEET 2 AA1 9 LEU A 134 LYS A 138 -1 O LEU A 134 N VAL A 127 SHEET 3 AA1 9 TYR A 97 ILE A 101 -1 N VAL A 98 O GLU A 137 SHEET 4 AA1 9 LEU A 87 THR A 93 -1 N VAL A 91 O ILE A 99 SHEET 5 AA1 9 LEU A 7 ALA A 14 1 N ALA A 14 O HIS A 92 SHEET 6 AA1 9 PRO A 178 GLY A 183 1 O VAL A 180 N HIS A 8 SHEET 7 AA1 9 VAL A 152 MET A 156 1 N PHE A 154 O THR A 179 SHEET 8 AA1 9 VAL A 197 SER A 200 1 O VAL A 197 N ILE A 155 SHEET 9 AA1 9 GLU A 161 LEU A 162 1 N GLU A 161 O LYS A 198 CISPEP 1 VAL A 127 PRO A 128 0 -25.05 CRYST1 113.240 113.240 102.820 90.00 90.00 120.00 H 3 2 18 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 0.008831 0.005098 0.000000 0.00000 SCALE2 0.000000 0.010197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009726 0.00000 CONECT 1874 1875 CONECT 1875 1874 1876 CONECT 1876 1875 1877 CONECT 1877 1876 1878 1881 CONECT 1878 1877 1883 CONECT 1879 1880 1881 1883 CONECT 1880 1879 CONECT 1881 1877 1879 1882 CONECT 1882 1881 CONECT 1883 1878 1879 1884 CONECT 1884 1883 1885 1893 CONECT 1885 1884 1886 CONECT 1886 1885 1887 CONECT 1887 1886 1888 1893 CONECT 1888 1887 1889 1890 CONECT 1889 1888 CONECT 1890 1888 1891 CONECT 1891 1890 1892 CONECT 1892 1891 1893 CONECT 1893 1884 1887 1892 CONECT 1894 1895 1896 CONECT 1895 1894 CONECT 1896 1894 1897 CONECT 1897 1896 CONECT 1898 1899 1900 CONECT 1899 1898 CONECT 1900 1898 1901 1902 CONECT 1901 1900 CONECT 1902 1900 1903 CONECT 1903 1902 CONECT 1904 1905 1906 CONECT 1905 1904 CONECT 1906 1904 1907 1908 CONECT 1907 1906 CONECT 1908 1906 1909 CONECT 1909 1908 CONECT 1910 1911 1912 1913 CONECT 1911 1910 CONECT 1912 1910 CONECT 1913 1910 MASTER 404 0 6 12 9 0 0 6 2002 1 40 18 END