HEADER TRANSFERASE 06-SEP-24 9JGC TITLE CRYSTAL STRUCTURE OF NEP1 IN COMPLEX WITH ADENOSINE FROM PYROCOCCUS TITLE 2 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 9JGC 1 JRNL REVDAT 1 12-MAR-25 9JGC 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. 2.01 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16216 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 848 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1195 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.2330 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 : 64 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00000 REMARK 3 B22 (A**2) : -1.00000 REMARK 3 B33 (A**2) : 3.24000 REMARK 3 B12 (A**2) : -0.50000 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): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.720 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1973 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1953 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2650 ; 1.472 ; 1.672 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4509 ; 0.515 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 227 ; 6.553 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 16 ;14.899 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 373 ;16.192 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 294 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2209 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 420 ; 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): 905 ; 1.779 ; 1.701 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 905 ; 1.765 ; 1.701 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1130 ; 2.857 ; 3.041 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1131 ; 2.856 ; 3.043 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1068 ; 3.002 ; 2.256 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1069 ; 3.001 ; 2.260 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1520 ; 4.732 ; 3.866 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2289 ; 7.890 ;19.660 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2262 ; 7.870 ;19.180 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): 18.8420 8.3209 18.9153 REMARK 3 T TENSOR REMARK 3 T11: 0.0669 T22: 0.1177 REMARK 3 T33: 0.0155 T12: -0.0188 REMARK 3 T13: -0.0221 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 1.8002 L22: 1.4032 REMARK 3 L33: 0.3401 L12: 0.2277 REMARK 3 L13: -0.1134 L23: -0.1403 REMARK 3 S TENSOR REMARK 3 S11: -0.0127 S12: -0.1337 S13: -0.0430 REMARK 3 S21: -0.0058 S22: 0.0338 S23: -0.0570 REMARK 3 S31: -0.0061 S32: -0.0614 S33: -0.0211 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 9JGC 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_1300051275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : 17065 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 70.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.40 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 13.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48400 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: 0.1M SODIUM CHLORIDE, 0.1M HEPES PH REMARK 280 7.5, 1.6M AMMONIUM SULFATE, MICROBATCH, 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 56.70500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.73865 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.06000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 56.70500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 32.73865 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.06000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 56.70500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 32.73865 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.06000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 56.70500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 32.73865 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.06000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 56.70500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 32.73865 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.06000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 56.70500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 32.73865 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 34.06000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 65.47729 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 68.12000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 65.47729 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 68.12000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 65.47729 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 68.12000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 65.47729 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 68.12000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 65.47729 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 68.12000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 65.47729 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 68.12000 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: 8880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 56.70500 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 32.73865 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.06000 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 501 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 512 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 529 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 434 O HOH A 481 2.10 REMARK 500 OE2 GLU A 2 O HOH A 401 2.18 REMARK 500 O HOH A 467 O HOH A 521 2.18 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 445 O HOH A 445 12555 1.83 REMARK 500 O HOH A 537 O HOH A 537 5555 2.10 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 ARG A 109 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = 3.1 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 LYS A 139 134.26 -172.86 REMARK 500 LYS A 177 52.76 -148.44 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 62 0.10 SIDE CHAIN REMARK 500 ARG A 65 0.09 SIDE CHAIN REMARK 500 ARG A 109 0.21 SIDE CHAIN REMARK 500 ARG A 203 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9JGC 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 ADN A 302 19 HET SO4 A 303 5 HET SO3 A 304 4 HET SO3 A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HET EDO A 309 4 HET EDO A 310 4 HET EDO A 311 4 HET PEG A 312 7 HETNAM CL CHLORIDE ION HETNAM ADN ADENOSINE HETNAM SO4 SULFATE ION HETNAM SO3 SULFITE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CL CL 1- FORMUL 3 ADN C10 H13 N5 O4 FORMUL 4 SO4 O4 S 2- FORMUL 5 SO3 2(O3 S 2-) FORMUL 7 EDO 6(C2 H6 O2) FORMUL 13 PEG C4 H10 O3 FORMUL 14 HOH *141(H2 O) HELIX 1 AA1 PRO A 20 LEU A 24 5 5 HELIX 2 AA2 HIS A 26 LYS A 37 1 12 HELIX 3 AA3 ARG A 39 ILE A 43 5 5 HELIX 4 AA4 ASP A 46 ARG A 55 1 10 HELIX 5 AA5 ARG A 65 ASP A 78 1 14 HELIX 6 AA6 SER A 79 GLU A 84 1 6 HELIX 7 AA7 ASN A 110 GLY A 125 1 16 HELIX 8 AA8 THR A 140 ASN A 149 1 10 HELIX 9 AA9 ILE A 164 ASP A 173 1 10 HELIX 10 AB1 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 TYR A 100 O ARG A 135 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 LEU A 9 O ARG A 88 SHEET 6 AA1 9 THR A 179 GLY A 183 1 O VAL A 180 N ILE A 10 SHEET 7 AA1 9 VAL A 153 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 VAL A 153 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 -17.09 CRYST1 113.410 113.410 102.180 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 0.008818 0.005091 0.000000 0.00000 SCALE2 0.000000 0.010182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009787 0.00000 CONECT 1880 1881 CONECT 1881 1880 1882 CONECT 1882 1881 1883 1884 CONECT 1883 1882 1888 CONECT 1884 1882 1885 1886 CONECT 1885 1884 CONECT 1886 1884 1887 1888 CONECT 1887 1886 CONECT 1888 1883 1886 1889 CONECT 1889 1888 1890 1898 CONECT 1890 1889 1891 CONECT 1891 1890 1892 CONECT 1892 1891 1893 1898 CONECT 1893 1892 1894 1895 CONECT 1894 1893 CONECT 1895 1893 1896 CONECT 1896 1895 1897 CONECT 1897 1896 1898 CONECT 1898 1889 1892 1897 CONECT 1899 1900 1901 1902 1903 CONECT 1900 1899 CONECT 1901 1899 CONECT 1902 1899 CONECT 1903 1899 CONECT 1904 1905 1906 1907 CONECT 1905 1904 CONECT 1906 1904 CONECT 1907 1904 CONECT 1908 1909 1910 1911 CONECT 1909 1908 CONECT 1910 1908 CONECT 1911 1908 CONECT 1912 1913 1914 CONECT 1913 1912 CONECT 1914 1912 1915 CONECT 1915 1914 CONECT 1916 1917 1918 CONECT 1917 1916 CONECT 1918 1916 1919 CONECT 1919 1918 CONECT 1920 1921 1922 CONECT 1921 1920 CONECT 1922 1920 1923 CONECT 1923 1922 CONECT 1924 1925 1926 CONECT 1925 1924 CONECT 1926 1924 1927 CONECT 1927 1926 CONECT 1928 1929 1930 CONECT 1929 1928 CONECT 1930 1928 1931 CONECT 1931 1930 CONECT 1932 1933 1934 CONECT 1933 1932 CONECT 1934 1932 1935 CONECT 1935 1934 CONECT 1936 1937 1938 CONECT 1937 1936 CONECT 1938 1936 1939 CONECT 1939 1938 1940 CONECT 1940 1939 1941 CONECT 1941 1940 1942 CONECT 1942 1941 MASTER 426 0 12 10 9 0 0 6 2076 1 63 18 END