HEADER TRANSPORT PROTEIN 24-APR-15 4ZGU TITLE CRYSTAL STRUCTURE OF MONOMER Y60W HCRBPII COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN II,CRBP-II; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RBP2, CRBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET17 KEYWDS 3D DOMAIN SWAPPING HUMAN CRBPII PROTEIN DIMERIZATION, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.NOSSONI,J.GEIGER REVDAT 4 06-MAR-24 4ZGU 1 REMARK REVDAT 3 25-DEC-19 4ZGU 1 REMARK REVDAT 2 06-SEP-17 4ZGU 1 JRNL REMARK REVDAT 1 08-JUN-16 4ZGU 0 JRNL AUTH Z.ASSAR,Z.NOSSONI,W.WANG,E.M.SANTOS,K.KRAMER,C.MCCORNACK, JRNL AUTH 2 C.VASILEIOU,B.BORHAN,J.H.GEIGER JRNL TITL DOMAIN-SWAPPED DIMERS OF INTRACELLULAR LIPID-BINDING JRNL TITL 2 PROTEINS: EVIDENCE FOR ORDERED FOLDING INTERMEDIATES. JRNL REF STRUCTURE V. 24 1590 2016 JRNL REFN ISSN 1878-4186 JRNL PMID 27524203 JRNL DOI 10.1016/J.STR.2016.05.022 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.NOSSONI,Z.ASSAR,M.NOSRATI,I.YAPICI,C.VASILEIOU,B.BORHAN, REMARK 1 AUTH 2 J.GEIGER REMARK 1 TITL STRUCTURES OF HOLO WILD-TYPE HUMAN CELLULAR RETINOL-BINDING REMARK 1 TITL 2 PROTEIN II (HCRBPII) BOUND TO RETINOL AND RETINAL REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 70 3226 2014 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 25478840 REMARK 1 DOI 10.1107/S1399004714023839 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 70382 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3749 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4814 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 234 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4314 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 391 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.859 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4445 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6000 ; 2.323 ; 1.919 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.968 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 239 ;36.147 ;25.021 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 786 ;15.510 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;21.300 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 646 ; 0.169 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3416 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2666 ; 1.691 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4272 ; 2.647 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1779 ; 3.775 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1728 ; 5.784 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4ZGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 4.2-4.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0781 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77520 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40800 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: NULL REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M CH3COONA.3H2O REMARK 280 PH4.6, 0.1M CH3COONH4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 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 GLU A 17 CG CD OE1 OE2 REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 ASP A 123 CG OD1 OD2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 TYR C 73 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS C 83 CG CD CE NZ REMARK 470 LYS C 98 CG CD CE NZ REMARK 470 LYS C 131 CG CD CE NZ REMARK 470 LYS C 133 CG CD CE NZ REMARK 470 LYS D 52 CG CD CE NZ REMARK 470 GLU D 102 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 12 N CA C O CB OG REMARK 480 SER C 76 CB OG REMARK 480 THR D 56 N CA C O CB OG1 CG2 REMARK 480 SER D 76 CB OG 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 C LYS D 133 O HOH D 305 1.59 REMARK 500 O HOH B 374 O HOH B 383 1.59 REMARK 500 O HOH A 362 O HOH A 390 1.67 REMARK 500 O HOH B 324 O HOH B 383 1.75 REMARK 500 O HOH B 301 O HOH B 368 1.82 REMARK 500 OD1 ASP B 47 O HOH B 301 1.93 REMARK 500 O HOH A 388 O HOH B 382 1.99 REMARK 500 OE2 GLU C 72 O ACT C 202 2.01 REMARK 500 CH2 TRP A 60 O HOH A 392 2.01 REMARK 500 O HOH B 337 O HOH B 387 2.03 REMARK 500 NZ LYS D 114 O HOH D 301 2.08 REMARK 500 CB LYS D 52 O HOH D 390 2.08 REMARK 500 O HOH A 306 O HOH A 362 2.08 REMARK 500 O HOH B 308 O HOH B 351 2.13 REMARK 500 OE2 GLU D 11 O HOH D 302 2.14 REMARK 500 CZ2 TRP A 60 O HOH A 392 2.16 REMARK 500 OG SER C 76 OE2 GLU D 111 2.16 REMARK 500 O HOH C 394 O HOH C 397 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 OD2 ASP B 47 OD2 ASP D 47 1554 1.56 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 SER A 12 CB SER A 12 OG -0.083 REMARK 500 SER A 12 C ASN A 13 N -0.198 REMARK 500 PHE A 130 CD1 PHE A 130 CE1 0.121 REMARK 500 SER C 76 CA SER C 76 CB 0.164 REMARK 500 GLU D 72 CB GLU D 72 CG -0.119 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 GLU A 11 O - C - N ANGL. DEV. = -13.0 DEGREES REMARK 500 SER A 12 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 ASN A 13 C - N - CA ANGL. DEV. = 24.3 DEGREES REMARK 500 LEU A 77 CB - CG - CD2 ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG A 104 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP B 45 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 45 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 123 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG C 2 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 SER C 76 CB - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 SER C 76 N - CA - CB ANGL. DEV. = -16.4 DEGREES REMARK 500 SER D 76 CB - CA - C ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG D 104 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 LYS D 132 CD - CE - NZ ANGL. DEV. = 17.6 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 SER A 12 142.54 -173.01 REMARK 500 SER A 12 117.33 -165.00 REMARK 500 LYS A 75 -139.67 63.84 REMARK 500 LEU B 77 -105.13 -111.46 REMARK 500 PHE C 57 -60.65 -108.61 REMARK 500 LEU C 77 -106.08 -133.54 REMARK 500 LEU C 77 -106.08 -114.61 REMARK 500 LEU D 77 -92.86 -139.84 REMARK 500 LEU D 77 -92.86 -123.41 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 ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 201 DBREF 4ZGU A 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 4ZGU B 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 4ZGU C 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 4ZGU D 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 4ZGU TRP A 60 UNP P50120 TYR 61 ENGINEERED MUTATION SEQADV 4ZGU TRP B 60 UNP P50120 TYR 61 ENGINEERED MUTATION SEQADV 4ZGU TRP C 60 UNP P50120 TYR 61 ENGINEERED MUTATION SEQADV 4ZGU TRP D 60 UNP P50120 TYR 61 ENGINEERED MUTATION SEQRES 1 A 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 A 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 133 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 A 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 A 133 THR THR SER THR PHE ARG ASN TRP ASP VAL ASP PHE THR SEQRES 6 A 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 A 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 A 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 A 133 GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 A 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 A 133 LYS LYS LYS SEQRES 1 B 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 B 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 B 133 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 B 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 B 133 THR THR SER THR PHE ARG ASN TRP ASP VAL ASP PHE THR SEQRES 6 B 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 B 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 B 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 B 133 GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 B 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 B 133 LYS LYS LYS SEQRES 1 C 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 C 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 C 133 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 C 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 C 133 THR THR SER THR PHE ARG ASN TRP ASP VAL ASP PHE THR SEQRES 6 C 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 C 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 C 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 C 133 GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 C 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 C 133 LYS LYS LYS SEQRES 1 D 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 D 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 D 133 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 D 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 D 133 THR THR SER THR PHE ARG ASN TRP ASP VAL ASP PHE THR SEQRES 6 D 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 D 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 D 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 D 133 GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 D 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 D 133 LYS LYS LYS HET ACT A 201 4 HET ACT A 202 4 HET ACT B 201 4 HET ACT B 202 4 HET ACT B 203 4 HET ACT C 201 4 HET ACT C 202 4 HET ACT D 201 4 HETNAM ACT ACETATE ION FORMUL 5 ACT 8(C2 H3 O2 1-) FORMUL 13 HOH *391(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASP A 26 LYS A 31 1 6 HELIX 3 AA3 ASN B 15 LEU B 23 1 9 HELIX 4 AA4 ASP B 26 VAL B 34 1 9 HELIX 5 AA5 ASN C 15 LEU C 23 1 9 HELIX 6 AA6 ASP C 26 VAL C 34 1 9 HELIX 7 AA7 ASN D 15 LEU D 23 1 9 HELIX 8 AA8 ASP D 26 LEU D 36 1 11 SHEET 1 AA110 ASN A 59 THR A 65 0 SHEET 2 AA110 ASN A 48 THR A 54 -1 N PHE A 49 O PHE A 64 SHEET 3 AA110 THR A 39 ASP A 45 -1 N VAL A 41 O LYS A 52 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O LYS A 40 SHEET 5 AA110 GLN A 124 LYS A 132 -1 O ARG A 127 N GLU A 14 SHEET 6 AA110 LYS A 114 CYS A 121 -1 N LEU A 119 O CYS A 126 SHEET 7 AA110 GLY A 105 GLU A 111 -1 N TRP A 109 O TYR A 116 SHEET 8 AA110 VAL A 92 LYS A 98 -1 N CYS A 95 O TRP A 106 SHEET 9 AA110 HIS A 81 GLU A 89 -1 N THR A 87 O VAL A 94 SHEET 10 AA110 PHE A 70 TYR A 73 -1 N PHE A 70 O ALA A 84 SHEET 1 AA210 ASN B 59 THR B 65 0 SHEET 2 AA210 ASN B 48 THR B 54 -1 N PHE B 49 O PHE B 64 SHEET 3 AA210 THR B 39 ASP B 45 -1 N ASP B 43 O LYS B 50 SHEET 4 AA210 GLY B 6 GLU B 14 -1 N TRP B 8 O LYS B 40 SHEET 5 AA210 GLN B 124 LYS B 132 -1 O VAL B 129 N GLU B 11 SHEET 6 AA210 LYS B 114 CYS B 121 -1 N LEU B 117 O GLN B 128 SHEET 7 AA210 GLY B 105 GLU B 111 -1 N TRP B 109 O TYR B 116 SHEET 8 AA210 VAL B 92 LYS B 98 -1 N CYS B 95 O TRP B 106 SHEET 9 AA210 HIS B 81 GLU B 89 -1 N THR B 87 O VAL B 94 SHEET 10 AA210 PHE B 70 TYR B 73 -1 N PHE B 70 O ALA B 84 SHEET 1 AA310 ASN C 59 THR C 65 0 SHEET 2 AA310 ASN C 48 THR C 54 -1 N THR C 53 O TRP C 60 SHEET 3 AA310 THR C 39 ASP C 45 -1 N ASP C 45 O ASN C 48 SHEET 4 AA310 GLY C 6 GLU C 14 -1 N GLY C 6 O ILE C 42 SHEET 5 AA310 GLN C 124 LYS C 132 -1 O VAL C 129 N GLU C 11 SHEET 6 AA310 LYS C 114 CYS C 121 -1 N LEU C 117 O GLN C 128 SHEET 7 AA310 GLY C 105 GLU C 111 -1 N TRP C 109 O TYR C 116 SHEET 8 AA310 VAL C 92 LYS C 98 -1 N CYS C 95 O TRP C 106 SHEET 9 AA310 HIS C 81 GLU C 89 -1 N LYS C 83 O LYS C 98 SHEET 10 AA310 PHE C 70 TYR C 73 -1 N PHE C 70 O ALA C 84 SHEET 1 AA410 ARG D 58 THR D 65 0 SHEET 2 AA410 ASN D 48 SER D 55 -1 N THR D 53 O TRP D 60 SHEET 3 AA410 THR D 39 ASP D 45 -1 N VAL D 41 O LYS D 52 SHEET 4 AA410 GLY D 6 GLU D 14 -1 N TRP D 8 O LYS D 40 SHEET 5 AA410 GLN D 124 LYS D 132 -1 O VAL D 129 N GLU D 11 SHEET 6 AA410 LYS D 114 CYS D 121 -1 N LEU D 117 O GLN D 128 SHEET 7 AA410 GLY D 105 GLU D 111 -1 N TRP D 109 O TYR D 116 SHEET 8 AA410 VAL D 92 LYS D 98 -1 N LEU D 93 O GLN D 108 SHEET 9 AA410 HIS D 81 GLU D 89 -1 N THR D 87 O VAL D 94 SHEET 10 AA410 PHE D 70 TYR D 73 -1 N PHE D 70 O ALA D 84 SITE 1 AC1 3 LYS A 40 TRP A 106 GLN A 108 SITE 1 AC2 5 GLN A 38 THR A 53 SER A 55 ARG A 58 SITE 2 AC2 5 HOH A 321 SITE 1 AC3 4 LYS B 40 THR B 51 TRP B 106 GLN B 108 SITE 1 AC4 2 ARG B 2 GLY B 90 SITE 1 AC5 4 LEU B 85 LYS B 98 VAL D 94 VAL D 96 SITE 1 AC6 3 LYS C 40 TRP C 106 GLN C 108 SITE 1 AC7 4 VAL C 62 GLU C 72 GLN C 97 TRP C 106 SITE 1 AC8 4 VAL D 62 GLU D 72 GLN D 97 TRP D 106 CRYST1 36.596 54.335 68.588 108.13 97.03 104.09 P 1 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 0.027325 0.006861 0.006201 0.00000 SCALE2 0.000000 0.018976 0.007189 0.00000 SCALE3 0.000000 0.000000 0.015709 0.00000